#NEXUS [written Mon Mar 13 15:22:17 EDT 2017 by Mesquite version 3.2 (build 801) at ag-plp-11ba0tj.ag.cornell.edu/132.236.30.46] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=16; TAXLABELS Puccinia_graminis_HQ317657 Puccinia_graminis_HQ317641_ Puccinia_coronata_var._avenae_f.sp._graminicola_HM147376 Puccinia_coronata_var._avenae_f.sp._graminicola_HM147373_ Puccinia_coronata_var._avenae_f.sp._avenae_HM147344_ Puccinia_coronata_var._avenae_f.sp._avenae_HM147354_ Puccinia_sp._Alder_buckthorn_CT Puccinia_coronata_var_coronata_HM147367 'Puccinia coronati-brevispora HM147359' 'Puccinia coronati-brevispora HM147377' 'Puccinia coronati-calamagrostidis HM147347 ' 'Puccinia coronati-calamagrostidis HM147375 ' 'Puccinia coronati-hordei HM147346 ' 'Puccinia coronati-agrostidis HM147345 ' 'Puccinia coronati-agrostidis HM147379 ' 'Puccinia coronati-japonica HM147378 ' ; END; BEGIN CHARACTERS; TITLE 'RPB2_ML'; DIMENSIONS NCHAR=306; FORMAT DATATYPE = DNA INTERLEAVE GAP = - MISSING = -; MATRIX Puccinia_graminis_HQ317657 AGACGTGTCGATGCCGCTGAAGTCGACGGAGAACGGGATCATCGACCAAG Puccinia_graminis_HQ317641_ AGACGTGTCGATGCCGCTGAAGTCGACGGAGAACGGGATCATCGACCAAG Puccinia_coronata_var._avenae_f.sp._graminicola_HM147376 GGACGTGTCGATGCCCTTGAAGTCGACGGAGAATGGGATTATCGATCAAG Puccinia_coronata_var._avenae_f.sp._graminicola_HM147373_ GGACGTGTCGATGCCCTTGAAGTCGACGGAGAATGGGATTATCGATCAAG Puccinia_coronata_var._avenae_f.sp._avenae_HM147344_ GGACGTGTCGATGCCCTTGAAGTCGACGGAGAATGGGATTATCGATCAAG Puccinia_coronata_var._avenae_f.sp._avenae_HM147354_ GGACGTGTCGATGCCCTTGAAGTCGACGGAGAATGGGATTATCGATCAAG Puccinia_sp._Alder_buckthorn_CT GGACGTGTCGATGCCCTTGAAGTCGACGGAGAATGGGATTATCGATCAAG Puccinia_coronata_var_coronata_HM147367 GGACGTGTCGATGCCCTTGAAGTCGACGGAGAATGGGATTATCGATCAAG 'Puccinia coronati-brevispora HM147359' ----------------------------------------ATCGATCAAG 'Puccinia coronati-brevispora HM147377' ----------------------------------------ATCGATCAAG 'Puccinia coronati-calamagrostidis HM147347 ' ----------------------------------------ATTGATCAGG 'Puccinia coronati-calamagrostidis HM147375 ' GGACGTCTCGATGCCTTTGAAATCAACGGAAAATGGGATTATCGATCAAG 'Puccinia coronati-hordei HM147346 ' ----------------------------------------ATCGATCAAG 'Puccinia coronati-agrostidis HM147345 ' GGACGTGTCGATGCCCTTGAAGTCGACGGAAAATGGGATTATCGATCAAG 'Puccinia coronati-agrostidis HM147379 ' GGACGTGTCGATGCCCTTGAAGTCGACGGAAAATGGGATTATCGATCAAG 'Puccinia coronati-japonica HM147378 ' ----------------------------------------ATCGATCAAG Puccinia_graminis_HQ317657 TCCTGGTGACGACGAACCAGGACGGACTGAAGTTTGTGAAGGTCCGGATC Puccinia_graminis_HQ317641_ TCCTGGTGACGACGAACCAGGACGGACTGAAGTTTGTGAAGGTCCGGATC Puccinia_coronata_var._avenae_f.sp._graminicola_HM147376 TCTTGGTGACGACCAACCAGGATGGATTGAAGTTTGTCAAGGTGCGGATT Puccinia_coronata_var._avenae_f.sp._graminicola_HM147373_ TCTTGGTGACGACCAACCAGGATGGATTGAAGTTTGTCAAGGTGCGGATT Puccinia_coronata_var._avenae_f.sp._avenae_HM147344_ TCTTGGTGACGACCAACCAGGATGGATTGAAGTTTGTCAAGGTGCGGATT Puccinia_coronata_var._avenae_f.sp._avenae_HM147354_ TCTTGGTGACGACCAACCAGGATGGATTGAAGTTTGTCAAGGTGCGGATT Puccinia_sp._Alder_buckthorn_CT TCTTGGTGACGACGAACCAGGATGGATTGAAGTTTGTCAAGGTGCGGATT Puccinia_coronata_var_coronata_HM147367 TCTTGGTGACGACGAACCAGGATGGATTGAAGTTTGTCAAGGTGCGGATT 'Puccinia coronati-brevispora HM147359' TCTTGGTGACGACCAACCAGGATGGATTGAAGTTTGTCAAGGTGAGGATT 'Puccinia coronati-brevispora HM147377' TCTTGGTGACGACCAACCAGGATGGATTGAAGTTTGTCAAGGTGAGGATT 'Puccinia coronati-calamagrostidis HM147347 ' TCTTRGTGACGACCAACCAGGAT-----GAAGTTTGTCAAGGTTCGGATT 'Puccinia coronati-calamagrostidis HM147375 ' TCTTAGTGACGACTAACCAGGATGGATTGAAGTTTGTCAAGGTTCGGATT 'Puccinia coronati-hordei HM147346 ' TCTTGGTGACGACCAACCAGGATGGATTGAAGTTTGTCAAGGTGAGGATT 'Puccinia coronati-agrostidis HM147345 ' TCTTGGTSACGACTAACCAGGATGGATTGAAGTTTGTCAAGGTGCGGATT 'Puccinia coronati-agrostidis HM147379 ' TCTTGGTGACGACTAACCAGGATGGATTGAAGTTTGTCAAGGTGCGGATT 'Puccinia coronati-japonica HM147378 ' TCTTGGTGACAACCAACCAGGATGGATTGAAGTTTGTCAAGGTGCGGATT Puccinia_graminis_HQ317657 CGCTCGACCCGGATCCCGGAGACCGGCGACAAGTTTGCATCCCGGCATGG Puccinia_graminis_HQ317641_ CGCTCGACCCGGATCCCGGAGACCGGCGACAAGTTTGCATCCCGGCATGG Puccinia_coronata_var._avenae_f.sp._graminicola_HM147376 CGCTCTACGCGTATTCCGGAGACGGGAGACAAGTTTGCGTCGCGACATGG Puccinia_coronata_var._avenae_f.sp._graminicola_HM147373_ CGCTCTACGCGTATTCCGGAGACGGGAGACAAGTTTGCGTCGCGACATGG Puccinia_coronata_var._avenae_f.sp._avenae_HM147344_ CGCTCTACGCGTATTCCGGAGACGGGAGACAAGTTTGCGTCGCGACATGG Puccinia_coronata_var._avenae_f.sp._avenae_HM147354_ CGCTCTACGCGTATTCCGGAGACGGGAGACAAGTTTGCGTCGCGACATGG Puccinia_sp._Alder_buckthorn_CT CGCTCTACGCGTATTCCGGAGACGGGAGACAAGTTTGCGTCGCGACATGG Puccinia_coronata_var_coronata_HM147367 CGCTCTACGCGTATTCCGGAGACGGGAGACAAGTTTGCGTCGCGACATGG 'Puccinia coronati-brevispora HM147359' CGCTCTACGCGTATCCCCGAGACGGGAGACAAGTTTGCTTCGCGGCATGG 'Puccinia coronati-brevispora HM147377' CGCTCTACGCGTATCCCCGAGACGGGAGACAAGTTTGCTTCGCGGCATGG 'Puccinia coronati-calamagrostidis HM147347 ' CGCTCYACGCGTATTCCTGAGACGGGAGACAAGTTTGCTTCGCGACAYGG 'Puccinia coronati-calamagrostidis HM147375 ' CGCTCCACGCGTATTCCTGAGACGGGAGACAAGTTTGCTTCGCGACATGG 'Puccinia coronati-hordei HM147346 ' CGCTCTACGCGTATCCCCGAAACGGGAGACAAGTTTGCTTCGCGGCAYGG 'Puccinia coronati-agrostidis HM147345 ' CGCTCTACGCGTATCCCCGAGACGGGAGACAAGTTTGCGTCGCGACATGG 'Puccinia coronati-agrostidis HM147379 ' CGCTCTACGCGTATCCCCGAGACGGGAGACAAGTTTGCGTCGCGACATGG 'Puccinia coronati-japonica HM147378 ' CGTTCTACGCGTATCCCGGAGACGGGAGACAAGTTTGCTTCGCGACATGG Puccinia_graminis_HQ317657 ACAGAAAGGGACGGTGGGGATCCTCTATCGTCAGGAAGACATGCCCTTCA Puccinia_graminis_HQ317641_ ACAGAAAGGGACGGTGGGGATCCTCTATCGTCAGGAAGACATGCCCTTCA Puccinia_coronata_var._avenae_f.sp._graminicola_HM147376 GCAGAAGGGTACGGTGGGGATCTTGTACCGACAGGAAGACATGCCGTTCA Puccinia_coronata_var._avenae_f.sp._graminicola_HM147373_ GCAGAAGGGTACGGTGGGGATCTTGTACCGACAGGAAGACATGCCGTTCA Puccinia_coronata_var._avenae_f.sp._avenae_HM147344_ GCAGAAGGGTACGGTGGGGATCTTGTACCGACAGGAAGACATGCCGTTCA Puccinia_coronata_var._avenae_f.sp._avenae_HM147354_ GCAGAAGGGTACGGTGGGGATCTTGTACCGACAGGAAGACATGCCGTTCA Puccinia_sp._Alder_buckthorn_CT GCAGAAGGGTACGGTGGGGATCTTGTACCGACAGGAAGACATGCCGTTCA Puccinia_coronata_var_coronata_HM147367 GCAGAAGGGTACGGTGGGGATCTTGTACCGACAGGAAGACATGCCGTTCA 'Puccinia coronati-brevispora HM147359' GCAGAAGGGCACAGTGGGGATCTTGTACCGACAGGAAGACATGCCGTTCA 'Puccinia coronati-brevispora HM147377' GCAGAAGGGCACAGTGGGGATCTTGTACCGACAGGAAGACATGCCGTTCA 'Puccinia coronati-calamagrostidis HM147347 ' GCAGAAGGGTACGGTGGGGATCCTGTACCGACAGGAAGACATGCCGTTTA 'Puccinia coronati-calamagrostidis HM147375 ' GCAGAAGGGGACGGTGGGGATCCTGTACCGACAGGAAGACATGCCGTTTA 'Puccinia coronati-hordei HM147346 ' GCAGAAGGGTACAGTGGGGATCTTGTACCGACAGGAAGACATGCCGTTCA 'Puccinia coronati-agrostidis HM147345 ' GCAGAAGGGTACGGTGGGGATCTTGTACCGACAGGAGGACATGCCATTCA 'Puccinia coronati-agrostidis HM147379 ' GCAGAAGGGTACGGTGGGGATCTTGTACCGACAGGAGGACATGCCATTCA 'Puccinia coronati-japonica HM147378 ' GCAGAAGGGTACGGTGGGGATCTTGTACCGACAGGAAGACATGCCGTTCA Puccinia_graminis_HQ317657 CCTCCGAAGGCGTGTGTCCAGATATCATCATCAACCCGCATGCTATTCCC Puccinia_graminis_HQ317641_ CCTCCGAAGGCGTGTGTCCAGATATCATCATCAACCCGCATGCTATCCCC Puccinia_coronata_var._avenae_f.sp._graminicola_HM147376 CCTCGGAGGGAATATGTCCGGACATCATCATCAACCCACATGCCATTCCG Puccinia_coronata_var._avenae_f.sp._graminicola_HM147373_ CCTCGGAGGGAATATGTCCGGACATCATCATCAACCCACATGCCATTCCG Puccinia_coronata_var._avenae_f.sp._avenae_HM147344_ CCTCGGAGGGAATATGTCCGGACATCATCATCAACCCACATGCCATTCCG Puccinia_coronata_var._avenae_f.sp._avenae_HM147354_ CCTCGGAGGGAATATGTCCGGACATCATCATCAACCCACATGCCATTCCG Puccinia_sp._Alder_buckthorn_CT CCTCGGAGGGAATATGTCCGGACATCATCATCAACCCACATGCCATTCCG Puccinia_coronata_var_coronata_HM147367 CCTCGGAGGGAATATGTCCGGACATCATCATCAACCCACATGCCATTCCG 'Puccinia coronati-brevispora HM147359' CCTCGGAGGGAATCTGTCCGGACATCATTATCAACCCACATGCCATTCCG 'Puccinia coronati-brevispora HM147377' CCTCGGAGGGAATCTGTCCGGACATCATTATCAACCCACATGCCATTCCG 'Puccinia coronati-calamagrostidis HM147347 ' CCTCGGAGGGMATCTGTCCGGACATCATCATCAACCCGCACGCCATTCCG 'Puccinia coronati-calamagrostidis HM147375 ' CCTCGGAGGGCATCTGTCCGGACATCATCATCAACCCGCACGCCATTCCG 'Puccinia coronati-hordei HM147346 ' CCTCGGAGGGAATCTGTCCGGACATCATCATCAACCCACATGCCATTCCG 'Puccinia coronati-agrostidis HM147345 ' CCTCGGAGGGAATCTGTCCGGACATCATTATCAACCCACATGCGATTCCG 'Puccinia coronati-agrostidis HM147379 ' CCTCGGAGGGAATCTGTCCGGACATCATTATCAACCCACATGCGATTCCG 'Puccinia coronati-japonica HM147378 ' CCTCGGAGGGAATCTGTCCGGACATTATCATCAACCCACATGCGATTCCG Puccinia_graminis_HQ317657 TCTCGAATGACCATCGGCCATCTCGTCGAATGTCTCTTGAGCAAAGTCTC Puccinia_graminis_HQ317641_ TCTCGAATGACCATCGGCCATCTCGTCGAATGTCTCTTGAGCAAAGTCTC Puccinia_coronata_var._avenae_f.sp._graminicola_HM147376 TCCCGGATGACGATTGGACATCTGGTCGAGTGTTTGCTCAGCAAGGTGTC Puccinia_coronata_var._avenae_f.sp._graminicola_HM147373_ TCCCGGATGACGATTGGACATCTGGTCGAGTGTTTGCTCAGCAAGGTGTC Puccinia_coronata_var._avenae_f.sp._avenae_HM147344_ TCCCGGATGACGATTGGACATCTGGTCGAGTGTTTGCTCAGCAAGGTGTC Puccinia_coronata_var._avenae_f.sp._avenae_HM147354_ TCCCGGATGACGATTGGACATCTGGTCGAGTGTTTGCTCAGCAAGGTGTC Puccinia_sp._Alder_buckthorn_CT TCCCGGATGACGATTGGACATCTGGTCGAGTGTTTGCTCAGCAAAGTGTC Puccinia_coronata_var_coronata_HM147367 TCCCGGATGACGATTGGACATCTGGTCGAGTGTTTGCTCAGCAAAGTGTC 'Puccinia coronati-brevispora HM147359' TCCCGGATGACGATCGGACATCTGGTGGAGTGTTTGCTGAGCAAGGTGTC 'Puccinia coronati-brevispora HM147377' TCCCGGATGACGATCGGACATCTGGTGGAGTGTTTGCTGAGCAAGGTGTC 'Puccinia coronati-calamagrostidis HM147347 ' TCCCGAATGACGATCGGACATCTGGTSGAATGTCTGCTCAGCAAGGTCTC 'Puccinia coronati-calamagrostidis HM147375 ' TCCCGAATGACGATCGGACATCTGGTAGAGTGTCTGCTCAGCAAGGTCTC 'Puccinia coronati-hordei HM147346 ' TCCCGGATGACGATCGGACATCTGGTAGAGTGTTTGCTGAGCAAGGTGTC 'Puccinia coronati-agrostidis HM147345 ' TCCCGGATGACGATCGGGCATCTGGTGGAGTGTTTGCTTAGCAAGGTCTC 'Puccinia coronati-agrostidis HM147379 ' TCCCGGATGACGATCGGGCAT----------------------------- 'Puccinia coronati-japonica HM147378 ' TCCCGGATGACAATTGGACATCTGGTGGAGTGTTTGCTCAGCAAGGTGTC Puccinia_graminis_HQ317657 GACAAT Puccinia_graminis_HQ317641_ GACAAT Puccinia_coronata_var._avenae_f.sp._graminicola_HM147376 GACGAT Puccinia_coronata_var._avenae_f.sp._graminicola_HM147373_ GACGAT Puccinia_coronata_var._avenae_f.sp._avenae_HM147344_ GACGAT Puccinia_coronata_var._avenae_f.sp._avenae_HM147354_ GACGAT Puccinia_sp._Alder_buckthorn_CT GACGAT Puccinia_coronata_var_coronata_HM147367 GACGAT 'Puccinia coronati-brevispora HM147359' GACGAT 'Puccinia coronati-brevispora HM147377' GACGAT 'Puccinia coronati-calamagrostidis HM147347 ' GACGAT 'Puccinia coronati-calamagrostidis HM147375 ' GACGAT 'Puccinia coronati-hordei HM147346 ' GACGAT 'Puccinia coronati-agrostidis HM147345 ' GACGAT 'Puccinia coronati-agrostidis HM147379 ' ------ 'Puccinia coronati-japonica HM147378 ' GACGAT ; END; BEGIN PAUP; factory; set criterion = likelihood; Lset base = equal nst = 6 rmat = ( 0.9278 7.5406 0.0004 4.0067 7.5406 ) rates = gamma shape = 0.2430 ncat = 4 pinvar = 0; END; BEGIN PAUP; outgroup HQ317641_Puccinia_graminis / only; set root = outgroup; set outroot = paraphyl; set maxtrees = 10000 increase = no autoclose = no torder = right tcompress = yes taxlabels = full storebrlens = yes storetreewts = yes; END; BEGIN PAUP; log file = Pc_RPB2_ML_March9.log; set autoclose = yes; hsearch start = stepwise addseq = random nreps = 1000 nchuck = 100 chuckscore = 1 savereps = yes randomize = addseq rstatus = yes hold = 1 swap = tbr multrees = yes; savetrees file = Pc_RPB2_ML_March9.all.tre brlen = yes; filter best = yes permdel = yes; savetrees file = Pc_RPB2_ML_March9.best.tre brlen = yes; log stop; END; begin paup; set storetreewts = yes; bootstrap nreps = 1000 treefile = Pc_RPB2_ML_March9.tre replace = no brlen = yes / start = stepwise addseq = random nreps = 10 savereps = no randomize = addseq hold = 1 swap = tbr multrees = yes; END; begin paup; gettrees allblocks = yes duptrees = keep storetreewts = yes storebrlens = yes mode = 7 file = Pc_RPB2_ML_March9.tre; END; begin paup; log file = Pc_RPB2_ML_March9.log; contree / majrule = yes strict = no le50 = yes usetreewts = yes showtree = yes treefile = Pc_RPB2_ML_March9_bootstrap.tre grpfreq = yes; log stop; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 306; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 306; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 306; END; BEGIN TREES; Title 'RPB2_ML'; ID 015ab9758a1f19; LINK Taxa = Taxa; TRANSLATE [0] 1 Puccinia_graminis_HQ317657, [1] 2 Puccinia_graminis_HQ317641_, [2] 3 Puccinia_coronata_var._avenae_f.sp._graminicola_HM147376, [3] 4 Puccinia_coronata_var._avenae_f.sp._graminicola_HM147373_, [4] 5 Puccinia_coronata_var._avenae_f.sp._avenae_HM147344_, [5] 6 Puccinia_coronata_var._avenae_f.sp._avenae_HM147354_, [6] 7 Puccinia_sp._Alder_buckthorn_CT, [7] 8 Puccinia_coronata_var_coronata_HM147367, [8] 9 'Puccinia coronati-brevispora HM147359', [9] 10 'Puccinia coronati-brevispora HM147377', [10] 11 'Puccinia coronati-calamagrostidis HM147347 ', [11] 12 'Puccinia coronati-calamagrostidis HM147375 ', [12] 13 'Puccinia coronati-hordei HM147346 ', [13] 14 'Puccinia coronati-agrostidis HM147345 ', [14] 15 'Puccinia coronati-agrostidis HM147379 ', [15] 16 'Puccinia coronati-japonica HM147378 '; TREE 'RPB2_ML' = ((1,((3,4,5,6,((((9,10),13),((11,12),(14,15))),16)),(7,8))),2); END;