#NEXUS [written Tue Mar 14 13:03:51 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 coronati-calamagrostidis HM147375 ' Puccinia_graminis_HQ317657_ Puccinia_coronata_var._avenae_f.sp._graminicola_HM147376_ Puccinia_coronata_var._avenae_f.sp._avenae_HM147344_ Puccinia_coronata_var._avenae_f.sp._graminicola_HM147373_ Puccinia_coronata_var._avenae_f.sp._avenae_HM147354_ Puccinia_coronata_var._coronata_HM147367_ Puccinia_sp._Alder_buckthorn_CT 'Puccinia coronati-brevispora HM147359 ' 'Puccinia coronati-brevispora HM147377 ' 'Puccinia coronati-calamagrostidis HM147347 ' Puccinia_graminis_HQ317641_ 'Puccinia coronati-hordei HM147346 ' 'Puccinia coronati-japonica HM147378 ' 'Puccinia coronati-agrostidis HM147345 ' 'Puccinia coronati-agrostidis HM147379 ' ; END; BEGIN CHARACTERS; TITLE 'RPB2_MP'; DIMENSIONS NCHAR=306; FORMAT DATATYPE = DNA INTERLEAVE GAP = - MISSING = -; MATRIX 'Puccinia coronati-calamagrostidis HM147375 ' GGACGTCTCGATGCCTTTGAAATCAACGGAAAATGGGATTATCGATCAAG Puccinia_graminis_HQ317657_ AGACGTGTCGATGCCGCTGAAGTCGACGGAGAACGGGATCATCGACCAAG Puccinia_coronata_var._avenae_f.sp._graminicola_HM147376_ GGACGTGTCGATGCCCTTGAAGTCGACGGAGAATGGGATTATCGATCAAG Puccinia_coronata_var._avenae_f.sp._avenae_HM147344_ GGACGTGTCGATGCCCTTGAAGTCGACGGAGAATGGGATTATCGATCAAG Puccinia_coronata_var._avenae_f.sp._graminicola_HM147373_ GGACGTGTCGATGCCCTTGAAGTCGACGGAGAATGGGATTATCGATCAAG Puccinia_coronata_var._avenae_f.sp._avenae_HM147354_ GGACGTGTCGATGCCCTTGAAGTCGACGGAGAATGGGATTATCGATCAAG Puccinia_coronata_var._coronata_HM147367_ GGACGTGTCGATGCCCTTGAAGTCGACGGAGAATGGGATTATCGATCAAG Puccinia_sp._Alder_buckthorn_CT GGACGTGTCGATGCCCTTGAAGTCGACGGAGAATGGGATTATCGATCAAG 'Puccinia coronati-brevispora HM147359 ' ----------------------------------------ATCGATCAAG 'Puccinia coronati-brevispora HM147377 ' ----------------------------------------ATCGATCAAG 'Puccinia coronati-calamagrostidis HM147347 ' ----------------------------------------ATTGATCAGG Puccinia_graminis_HQ317641_ AGACGTGTCGATGCCGCTGAAGTCGACGGAGAACGGGATCATCGACCAAG 'Puccinia coronati-hordei HM147346 ' ----------------------------------------ATCGATCAAG 'Puccinia coronati-japonica HM147378 ' ----------------------------------------ATCGATCAAG 'Puccinia coronati-agrostidis HM147345 ' GGACGTGTCGATGCCCTTGAAGTCGACGGAAAATGGGATTATCGATCAAG 'Puccinia coronati-agrostidis HM147379 ' GGACGTGTCGATGCCCTTGAAGTCGACGGAAAATGGGATTATCGATCAAG 'Puccinia coronati-calamagrostidis HM147375 ' TCTTAGTGACGACTAACCAGGATGGATTGAAGTTTGTCAAGGTTCGGATT Puccinia_graminis_HQ317657_ TCCTGGTGACGACGAACCAGGACGGACTGAAGTTTGTGAAGGTCCGGATC Puccinia_coronata_var._avenae_f.sp._graminicola_HM147376_ TCTTGGTGACGACCAACCAGGATGGATTGAAGTTTGTCAAGGTGCGGATT Puccinia_coronata_var._avenae_f.sp._avenae_HM147344_ TCTTGGTGACGACCAACCAGGATGGATTGAAGTTTGTCAAGGTGCGGATT Puccinia_coronata_var._avenae_f.sp._graminicola_HM147373_ TCTTGGTGACGACCAACCAGGATGGATTGAAGTTTGTCAAGGTGCGGATT Puccinia_coronata_var._avenae_f.sp._avenae_HM147354_ TCTTGGTGACGACCAACCAGGATGGATTGAAGTTTGTCAAGGTGCGGATT Puccinia_coronata_var._coronata_HM147367_ TCTTGGTGACGACGAACCAGGATGGATTGAAGTTTGTCAAGGTGCGGATT Puccinia_sp._Alder_buckthorn_CT TCTTGGTGACGACGAACCAGGATGGATTGAAGTTTGTCAAGGTGCGGATT 'Puccinia coronati-brevispora HM147359 ' TCTTGGTGACGACCAACCAGGATGGATTGAAGTTTGTCAAGGTGAGGATT 'Puccinia coronati-brevispora HM147377 ' TCTTGGTGACGACCAACCAGGATGGATTGAAGTTTGTCAAGGTGAGGATT 'Puccinia coronati-calamagrostidis HM147347 ' TCTTRGTGACGACCAACCAGGAT-----GAAGTTTGTCAAGGTTCGGATT Puccinia_graminis_HQ317641_ TCCTGGTGACGACGAACCAGGACGGACTGAAGTTTGTGAAGGTCCGGATC 'Puccinia coronati-hordei HM147346 ' TCTTGGTGACGACCAACCAGGATGGATTGAAGTTTGTCAAGGTGAGGATT 'Puccinia coronati-japonica HM147378 ' TCTTGGTGACAACCAACCAGGATGGATTGAAGTTTGTCAAGGTGCGGATT 'Puccinia coronati-agrostidis HM147345 ' TCTTGGTSACGACTAACCAGGATGGATTGAAGTTTGTCAAGGTGCGGATT 'Puccinia coronati-agrostidis HM147379 ' TCTTGGTGACGACTAACCAGGATGGATTGAAGTTTGTCAAGGTGCGGATT 'Puccinia coronati-calamagrostidis HM147375 ' CGCTCCACGCGTATTCCTGAGACGGGAGACAAGTTTGCTTCGCGACATGG Puccinia_graminis_HQ317657_ CGCTCGACCCGGATCCCGGAGACCGGCGACAAGTTTGCATCCCGGCATGG Puccinia_coronata_var._avenae_f.sp._graminicola_HM147376_ CGCTCTACGCGTATTCCGGAGACGGGAGACAAGTTTGCGTCGCGACATGG Puccinia_coronata_var._avenae_f.sp._avenae_HM147344_ CGCTCTACGCGTATTCCGGAGACGGGAGACAAGTTTGCGTCGCGACATGG Puccinia_coronata_var._avenae_f.sp._graminicola_HM147373_ CGCTCTACGCGTATTCCGGAGACGGGAGACAAGTTTGCGTCGCGACATGG Puccinia_coronata_var._avenae_f.sp._avenae_HM147354_ CGCTCTACGCGTATTCCGGAGACGGGAGACAAGTTTGCGTCGCGACATGG Puccinia_coronata_var._coronata_HM147367_ CGCTCTACGCGTATTCCGGAGACGGGAGACAAGTTTGCGTCGCGACATGG Puccinia_sp._Alder_buckthorn_CT CGCTCTACGCGTATTCCGGAGACGGGAGACAAGTTTGCGTCGCGACATGG 'Puccinia coronati-brevispora HM147359 ' CGCTCTACGCGTATCCCCGAGACGGGAGACAAGTTTGCTTCGCGGCATGG 'Puccinia coronati-brevispora HM147377 ' CGCTCTACGCGTATCCCCGAGACGGGAGACAAGTTTGCTTCGCGGCATGG 'Puccinia coronati-calamagrostidis HM147347 ' CGCTCYACGCGTATTCCTGAGACGGGAGACAAGTTTGCTTCGCGACAYGG Puccinia_graminis_HQ317641_ CGCTCGACCCGGATCCCGGAGACCGGCGACAAGTTTGCATCCCGGCATGG 'Puccinia coronati-hordei HM147346 ' CGCTCTACGCGTATCCCCGAAACGGGAGACAAGTTTGCTTCGCGGCAYGG 'Puccinia coronati-japonica HM147378 ' CGTTCTACGCGTATCCCGGAGACGGGAGACAAGTTTGCTTCGCGACATGG 'Puccinia coronati-agrostidis HM147345 ' CGCTCTACGCGTATCCCCGAGACGGGAGACAAGTTTGCGTCGCGACATGG 'Puccinia coronati-agrostidis HM147379 ' CGCTCTACGCGTATCCCCGAGACGGGAGACAAGTTTGCGTCGCGACATGG 'Puccinia coronati-calamagrostidis HM147375 ' GCAGAAGGGGACGGTGGGGATCCTGTACCGACAGGAAGACATGCCGTTTA Puccinia_graminis_HQ317657_ ACAGAAAGGGACGGTGGGGATCCTCTATCGTCAGGAAGACATGCCCTTCA Puccinia_coronata_var._avenae_f.sp._graminicola_HM147376_ GCAGAAGGGTACGGTGGGGATCTTGTACCGACAGGAAGACATGCCGTTCA Puccinia_coronata_var._avenae_f.sp._avenae_HM147344_ GCAGAAGGGTACGGTGGGGATCTTGTACCGACAGGAAGACATGCCGTTCA Puccinia_coronata_var._avenae_f.sp._graminicola_HM147373_ GCAGAAGGGTACGGTGGGGATCTTGTACCGACAGGAAGACATGCCGTTCA Puccinia_coronata_var._avenae_f.sp._avenae_HM147354_ GCAGAAGGGTACGGTGGGGATCTTGTACCGACAGGAAGACATGCCGTTCA Puccinia_coronata_var._coronata_HM147367_ GCAGAAGGGTACGGTGGGGATCTTGTACCGACAGGAAGACATGCCGTTCA Puccinia_sp._Alder_buckthorn_CT GCAGAAGGGTACGGTGGGGATCTTGTACCGACAGGAAGACATGCCGTTCA 'Puccinia coronati-brevispora HM147359 ' GCAGAAGGGCACAGTGGGGATCTTGTACCGACAGGAAGACATGCCGTTCA 'Puccinia coronati-brevispora HM147377 ' GCAGAAGGGCACAGTGGGGATCTTGTACCGACAGGAAGACATGCCGTTCA 'Puccinia coronati-calamagrostidis HM147347 ' GCAGAAGGGTACGGTGGGGATCCTGTACCGACAGGAAGACATGCCGTTTA Puccinia_graminis_HQ317641_ ACAGAAAGGGACGGTGGGGATCCTCTATCGTCAGGAAGACATGCCCTTCA 'Puccinia coronati-hordei HM147346 ' GCAGAAGGGTACAGTGGGGATCTTGTACCGACAGGAAGACATGCCGTTCA 'Puccinia coronati-japonica HM147378 ' GCAGAAGGGTACGGTGGGGATCTTGTACCGACAGGAAGACATGCCGTTCA 'Puccinia coronati-agrostidis HM147345 ' GCAGAAGGGTACGGTGGGGATCTTGTACCGACAGGAGGACATGCCATTCA 'Puccinia coronati-agrostidis HM147379 ' GCAGAAGGGTACGGTGGGGATCTTGTACCGACAGGAGGACATGCCATTCA 'Puccinia coronati-calamagrostidis HM147375 ' CCTCGGAGGGCATCTGTCCGGACATCATCATCAACCCGCACGCCATTCCG Puccinia_graminis_HQ317657_ CCTCCGAAGGCGTGTGTCCAGATATCATCATCAACCCGCATGCTATTCCC Puccinia_coronata_var._avenae_f.sp._graminicola_HM147376_ CCTCGGAGGGAATATGTCCGGACATCATCATCAACCCACATGCCATTCCG Puccinia_coronata_var._avenae_f.sp._avenae_HM147344_ CCTCGGAGGGAATATGTCCGGACATCATCATCAACCCACATGCCATTCCG Puccinia_coronata_var._avenae_f.sp._graminicola_HM147373_ CCTCGGAGGGAATATGTCCGGACATCATCATCAACCCACATGCCATTCCG Puccinia_coronata_var._avenae_f.sp._avenae_HM147354_ CCTCGGAGGGAATATGTCCGGACATCATCATCAACCCACATGCCATTCCG Puccinia_coronata_var._coronata_HM147367_ CCTCGGAGGGAATATGTCCGGACATCATCATCAACCCACATGCCATTCCG Puccinia_sp._Alder_buckthorn_CT CCTCGGAGGGAATATGTCCGGACATCATCATCAACCCACATGCCATTCCG 'Puccinia coronati-brevispora HM147359 ' CCTCGGAGGGAATCTGTCCGGACATCATTATCAACCCACATGCCATTCCG 'Puccinia coronati-brevispora HM147377 ' CCTCGGAGGGAATCTGTCCGGACATCATTATCAACCCACATGCCATTCCG 'Puccinia coronati-calamagrostidis HM147347 ' CCTCGGAGGGMATCTGTCCGGACATCATCATCAACCCGCACGCCATTCCG Puccinia_graminis_HQ317641_ CCTCCGAAGGCGTGTGTCCAGATATCATCATCAACCCGCATGCTATCCCC 'Puccinia coronati-hordei HM147346 ' CCTCGGAGGGAATCTGTCCGGACATCATCATCAACCCACATGCCATTCCG 'Puccinia coronati-japonica HM147378 ' CCTCGGAGGGAATCTGTCCGGACATTATCATCAACCCACATGCGATTCCG 'Puccinia coronati-agrostidis HM147345 ' CCTCGGAGGGAATCTGTCCGGACATCATTATCAACCCACATGCGATTCCG 'Puccinia coronati-agrostidis HM147379 ' CCTCGGAGGGAATCTGTCCGGACATCATTATCAACCCACATGCGATTCCG 'Puccinia coronati-calamagrostidis HM147375 ' TCCCGAATGACGATCGGACATCTGGTAGAGTGTCTGCTCAGCAAGGTCTC Puccinia_graminis_HQ317657_ TCTCGAATGACCATCGGCCATCTCGTCGAATGTCTCTTGAGCAAAGTCTC Puccinia_coronata_var._avenae_f.sp._graminicola_HM147376_ TCCCGGATGACGATTGGACATCTGGTCGAGTGTTTGCTCAGCAAGGTGTC Puccinia_coronata_var._avenae_f.sp._avenae_HM147344_ TCCCGGATGACGATTGGACATCTGGTCGAGTGTTTGCTCAGCAAGGTGTC Puccinia_coronata_var._avenae_f.sp._graminicola_HM147373_ TCCCGGATGACGATTGGACATCTGGTCGAGTGTTTGCTCAGCAAGGTGTC Puccinia_coronata_var._avenae_f.sp._avenae_HM147354_ TCCCGGATGACGATTGGACATCTGGTCGAGTGTTTGCTCAGCAAGGTGTC Puccinia_coronata_var._coronata_HM147367_ TCCCGGATGACGATTGGACATCTGGTCGAGTGTTTGCTCAGCAAAGTGTC Puccinia_sp._Alder_buckthorn_CT TCCCGGATGACGATTGGACATCTGGTCGAGTGTTTGCTCAGCAAAGTGTC 'Puccinia coronati-brevispora HM147359 ' TCCCGGATGACGATCGGACATCTGGTGGAGTGTTTGCTGAGCAAGGTGTC 'Puccinia coronati-brevispora HM147377 ' TCCCGGATGACGATCGGACATCTGGTGGAGTGTTTGCTGAGCAAGGTGTC 'Puccinia coronati-calamagrostidis HM147347 ' TCCCGAATGACGATCGGACATCTGGTSGAATGTCTGCTCAGCAAGGTCTC Puccinia_graminis_HQ317641_ TCTCGAATGACCATCGGCCATCTCGTCGAATGTCTCTTGAGCAAAGTCTC 'Puccinia coronati-hordei HM147346 ' TCCCGGATGACGATCGGACATCTGGTAGAGTGTTTGCTGAGCAAGGTGTC 'Puccinia coronati-japonica HM147378 ' TCCCGGATGACAATTGGACATCTGGTGGAGTGTTTGCTCAGCAAGGTGTC 'Puccinia coronati-agrostidis HM147345 ' TCCCGGATGACGATCGGGCATCTGGTGGAGTGTTTGCTTAGCAAGGTCTC 'Puccinia coronati-agrostidis HM147379 ' TCCCGGATGACGATCGGGCAT----------------------------- 'Puccinia coronati-calamagrostidis HM147375 ' GACGAT Puccinia_graminis_HQ317657_ GACAAT Puccinia_coronata_var._avenae_f.sp._graminicola_HM147376_ GACGAT Puccinia_coronata_var._avenae_f.sp._avenae_HM147344_ GACGAT Puccinia_coronata_var._avenae_f.sp._graminicola_HM147373_ GACGAT Puccinia_coronata_var._avenae_f.sp._avenae_HM147354_ GACGAT Puccinia_coronata_var._coronata_HM147367_ GACGAT Puccinia_sp._Alder_buckthorn_CT GACGAT 'Puccinia coronati-brevispora HM147359 ' GACGAT 'Puccinia coronati-brevispora HM147377 ' GACGAT 'Puccinia coronati-calamagrostidis HM147347 ' GACGAT Puccinia_graminis_HQ317641_ GACAAT 'Puccinia coronati-hordei HM147346 ' GACGAT 'Puccinia coronati-japonica HM147378 ' GACGAT 'Puccinia coronati-agrostidis HM147345 ' GACGAT 'Puccinia coronati-agrostidis HM147379 ' ------ ; END; BEGIN PAUP; Lset base = equal nst = 6 rmat = ( 0.9168 7.4185 0.0004 3.9349 7.4185 ) rates = gamma shape = 0.2470 ncat = 4 pinvar = 0; END; BEGIN PAUP; factory; set criterion = likelihood; Lset base = equal nst = 6 rmat = ( 2.0998 14.0836 0.0028 13.6693 27.3397 ) rates = gamma shape = 0.1920 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_March8.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_March8.all.tre brlen = yes; filter best = yes permdel = yes; savetrees file = Pc_RPB2_March8.best.tre brlen = yes; log stop; END; begin paup; set storetreewts = yes; bootstrap nreps = 1000 treefile = Pc_RPB2_March8.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_March8.tre; END; begin paup; log file = Pc_RPB2_March8.log; contree / majrule = yes strict = no le50 = yes usetreewts = yes showtree = yes treefile = Pc_RPB2_March8_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_MP'; ID 015ab39aeaae1; LINK Taxa = Taxa; TRANSLATE [0] 1 'Puccinia coronati-calamagrostidis HM147375 ', [1] 2 Puccinia_graminis_HQ317657_, [2] 3 Puccinia_coronata_var._avenae_f.sp._graminicola_HM147376_, [3] 4 Puccinia_coronata_var._avenae_f.sp._avenae_HM147344_, [4] 5 Puccinia_coronata_var._avenae_f.sp._graminicola_HM147373_, [5] 6 Puccinia_coronata_var._avenae_f.sp._avenae_HM147354_, [6] 7 Puccinia_coronata_var._coronata_HM147367_, [7] 8 Puccinia_sp._Alder_buckthorn_CT, [8] 9 'Puccinia coronati-brevispora HM147359 ', [9] 10 'Puccinia coronati-brevispora HM147377 ', [10] 11 'Puccinia coronati-calamagrostidis HM147347 ', [11] 12 Puccinia_graminis_HQ317641_, [12] 13 'Puccinia coronati-hordei HM147346 ', [13] 14 'Puccinia coronati-japonica HM147378 ', [14] 15 'Puccinia coronati-agrostidis HM147345 ', [15] 16 'Puccinia coronati-agrostidis HM147379 '; TREE 'RPB2_MP' = ((2,((((3,5,4,6),(8,7)),((((9,10),13),(15,16)),14)),(11,1))),12); END;