#NEXUS [written Wed Jul 24 16:14:13 GMT+00:00 2013 by Mesquite version 2.75 (build 566) at Macintosh-6.local/192.168.5.142] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=15; TAXLABELS Linocarpon_livistonae_DQ810207_ F530 Erythromada_lanciospora_DQ231442_ Linocarpon_elaeidis_DQ810222_ Zignoella_pulviscula_AF466091_ Striatosphaeria_codinaeophora_AF178546_ Lasiosphaeriella_nitida_HM171283_ Camarops_ustulinoides_AY346267_ Camarops_tubulina_AY346266_ Leptosporella_gregaria_HM171289_ Linocarpon_appendiculatum_AY346291_ Caudatispora_biapiculata_AY346269_ Helminthosphaeria_clavariarum_AY346283_ Lasiosphaeriella_pseudobombarda_HM171286_ Lasiosphaeriella_noonae_daniae_HM171284_ ; END; BEGIN CHARACTERS; TITLE ErythromadaMB; DIMENSIONS NCHAR=535; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Linocarpon_livistonae_DQ810207_ -----------------------------------------------ATTGCCTTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCT-TC-----------GGCCCGAGTTGTAATTTGTAGAGGATGCCTTGGTGG-GTGCT-CTTGTCTGAGTTCCCTGGAACAGGACGTCTTAAAGGGTGAGAATCCCGTAAAGAGTTGGACA-CCAAGCCTATGT-AAGGCTCTTTCCAAGAATCGAGTAGTTTGGGAATGCAGCTCTAAATGGGTGGTAAATTCCATCTAAAGCTAAATATTGGCGAGAGACCGATAGCGAACAAGTACAGTGAT-GAAAGATGAAAAGCACTTTGAAAAGAAAGTGAAAAAGTACGTGGAATTGTTGAAAGGGAAGCGTTTGAGA-CCAG-ACTCGT-GCCCTGTGAATCACCTTGCCTT--CT-GG-CGGGGCACTTCG-CAGCTTAT-CGGGCCAGCATC-GGTT-CTCGCA-GGGGGAT-AATGGCTTCAGGAATGTGACTT F530 GCTGAACTTAAGCATATCAATAAGCGCAGGAAAAGAAACCAACAGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACAGCTCAGATTTGAAAGCT--CCCCCC----CCC---GGGGCGCGTTGTAATCTGTAGAGGACG-TTT-CGGGCGCGGC-CTTGCCTAAGTCCCCTGGAACGGGGCGCCACAGAGGGTGAGAGCCCCGTAT--CGGCAGCGG-CCTAGCCTGTGTGAA-GCTCCTTCGACGAGTCGAGTAGTTTGGGATTGCTGCTCTAAATGGGAGGTAAATTCCTTCTAAAGCTAAATATTGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGGAAAGAGGGTTAAATAGCACGTGAAATTGCTGAAAGGGAAGCGCTAGTGA-TCAG-ACAC-TGGCAGGCGCGATCAGCCGGCGTT--CTCGC-CGGTGCACT-CG-TGGCTG-TCCGGGCTAGCGTC-GGTTTCTCT---GGGGGTGGAATAGCCC-GGGAAAGTAGCT- Erythromada_lanciospora_DQ231442_ GCTGAACTTAAGCATATCAATAAGCGCAGGAAAAGAAACCAACAGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACAGCTCAGATTTGAAAGC--GCCC------GCC---AGGA-CGCGTTGTAATCTGTAGAGGACG-CTT-CGGGCGACGC-CCCGCCTAAGTCCCCTGGAACGGGGCGCCACAGAGGGTGAGAGCCCCGTG---AGGCGGCGG-CCGGTCCCGCGTGAA-GCTCCCTCGACGAGTCGAGTAGTTTGGGATTGCTGCTCTAAATGGGAGGTACATTCCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAACAGTACGTGAAATTGCTGAAAGGGAAGCGCTCGTGA-CCAG-ACTTGC-GCGGGCGCGATCATCCGGCGTT--CTCGC-CGGTGCCCT-CG-CGCCCGCT-CAGGCCAGCGTC-GGTT-CCGCG--GGCGGTAGAAGAGCGC-GGGAATGTGGCTC Linocarpon_elaeidis_DQ810222_ -----------------------------------------------ATTGCCCTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCT-TC-----------GGCCCGAGTTGTAATTTGTAGAGGATG-CTT-TTGGTGCGGT-GCCTTCTGAGTTCCCTGTAACGGGACGCCTTAGAGGGTGAGAGCCCCGTAA--AGTTGGACA-CCAAGCCTATGTAAA-GCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCAAAATGGGAGGTAAATTTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAAAAGTACGTGAAATTGTTGAAAGGGAAGCGCTTATGA-CCAG-ACTTGT-GCCCTGCGGATCATCCAGCCTT--CTGGC-TGGTGCACTTCG-CT-TGGTT-CAGGCCAGCATC-GGTT-CTCTGA-GGGGGAT-AAAAGCTTCAGGGACGTGGCTC Zignoella_pulviscula_AF466091_ -------------ATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCCCT-----------AGGCCCGAGTTGTAATTTGCAGAGGATG-CTT-CCGGTGCGGC-GCCGTCCAAGTCCCCTGGAACGGGGTGCCACAGAGGGTGAGAGCCCCGTCG--GGTCGGCCG-CCAAGCCTATGTGAA-GCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTAGACCCCTTCTAAAGCTAAATATTGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAACAGTACGTGAAATTGTTGAAAGGGAAGCGCTTGTGA-CCAG-ACGTGC-GCCGGGT-GTTCAGCGGGCGTT--CTCGC-CCGTCTACT-CG-CCCTGGCG-CAGGCCAGCGTC-GGTT-CGGA-TGGGTGGAC-AAAGGTACCAGGAACGTGGCTC Striatosphaeria_codinaeophora_AF178546_ GCTGAACTTAAGCATATCAATAAGC?GAG?AAAAGAAACCAACATGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCCCC------------GGCCCGAGTTGTAATTTGCAGAGGATG-CTT-CCGGCAACGC-GCCTTCCAAGTCCCCTGGAACGGGGCGCCACAGAGGGTGAGAGCCCCGTCC--GGTCGGCCG-CCGCGCCTGTGCGAA-GCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAACGGGAGGTAGACCCCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAACAGTACGTGAAATTGTTGAAAGGGAAGCGCTCGGGA-CCAG-ACGTGC-GCCGGGC-GTTCAGCGGGCGTT--CTCGC-CCGTGTACT-CG-CCCCGGCG-CAGGCCAGCGTC-GGCT-C-GGGA-GGGGGAC-AAGGGCGCTGGGAACGTGGCTC Lasiosphaeriella_nitida_HM171283_ GCTGAACTTAAGCATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACGGCTCAAATTTGAAATCCGGCCCCCC--------GGGGCCCGAGTTGTAATTTGTAGAGGACG-CTT-CTGGCACGGC-ACCTTCCAAGTCCTCTGGAACGGGGCGCCGCAGAGGGTGAGAGCCCCGTAC--GGTCGGACG-CCAGGCCAGTGTGAA-GCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCAAAGTGGGAGGTAAATTCCTTCTAAAGCTAAATACCGGCTAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAACAGCACGTGAAATTGTTGAAAGGGAAGCGCTCATGA-CCAG-ACGTGC-GCCCCGCGGATCACCCGGCGTT--CTCGC-CGGCGCACTCCG-CGG-GGCG-CAGGCCAGCATC-GGTT-CTCGCG-GGGGGAC-AAAAGCCCGGGGAACGTGGCTC Camarops_ustulinoides_AY346267_ -----ACTTAAGCATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCC-TC-----------GGCCCGAGTTGTAATTTGCAGAGGATG-CTT-TTGGCGCGGC-GCCTCCCGAGTCCCCTGGAACGGGGCGCCACAGAGGGTGAGAGCCCCGTAT--GGTAGGACG-CCTAGCCTGTGTAAA-GCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCAAAATGGGAGGTAAATTCCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTCAAACAGCACGTGAAATTGTTGAAAGGGAAGCGCTCGTGA-CCAG-ACTTGC-GCCGGGTCGATCATCCGGTGTT--CTCAC-CGGTGCACT-CGGCCC-GGCT-CAGGCCAGCATC-GGTT-TTCGCG-GGGGGAT-AAAAGCCCGGGGAACGTGGCTC Camarops_tubulina_AY346266_ -----ACTTAAGCATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCC-TC-----------GGCCCGAGTTGTAATTTGCAGAGGATGTTTT-C-GGCGCGGC-GCCTCCCGAGTCCCCTGGAACGGGGCGCCACAGAGGGTGAGAGCCCCGTAT--GGTAGGACG-CCTAGCCTGTGTAAA-GCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCAAAATGGGAGGTAAATTCCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTCAAACAGCACGTGAAATTGTTGAAAGGGAAGCGCTCGTGA-CCAG-ACTTGC-GCCGGGCCGATCATCCGGTGTT--CTCAC-CGGTGCACT-CGGCCC-GGCT-CAGGCCAGCATC-GGTT-TTCGCG-GGGGGAC-AAAAGCCCGGGGAACGTGGCTC Leptosporella_gregaria_HM171289_ GCTGAACTTAAGCATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCCTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCCCCC----------GGGCCCGAGTTGTAATTTGCAGAGGATG-CTT-CGGGCGCGGT-GCCTTCCGAGTCCCCTGGAACGGGGCGCCATAGAGGGTGAGAGCCCCGTAC--GGTTGGACG-CCTAGCCCGTGTGAA-GCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCAAAATGGGAGGTAAGTTCCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGCACGTGAAATTGCTGAAAGGGAAGCGCTCGTGA-CCAG-ACGCGC-GCCGGGCGGATCATCCAGCGTT--CTCGC-TGGTGCACTCCG-CCC-GGCG-CGGGCCAGCGTC-GGTT-CTCGCG-GGGGGGC-AAAGGCGCCGGGAACGTAGCTC Linocarpon_appendiculatum_AY346291_ --T-AACTTAAGCATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCCCCCC---GCCCGGGGGCCCGAGTTGTAATTTGCAGAGGATG-CTT-CGGGCGCGGCGGCCTTCTGAGTCCCCTGGAACGGGGCGCCGCAGAGGGTGAGAGCCCCGTAC--CGTCGGCCG-CCAAGCCCGCGTGAA-GCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCAAAATGGGAGGTAAATTTCTTCTACAGCTAAATACCGGCTAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAACAGCACGTGAAATTGTTGAAAGGGAAGCGCCTGTGG-CCAG-ACGTGC-GCCGGGCGGATCACCCAGCGTT--CTCGC-TGGTGCACTCCG-CCC-GGCG-CAGGCCAGCATC-GGTT-CCCGCG-GGGGGAC-AAAAGCGCCGGGAACGTAGCTC Caudatispora_biapiculata_AY346269_ -CTG-ACTTAAGCATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCCCCCCA--GC---GGGGCCCGAGTTGTAATTTGGAGAGGACG-CTT-CTGGCGCGGC-CCCGTCCGAGTCCCCTGGAACGGGGCGCCGCAGAGGGTGAGAGCCCCGTAC--GGTCGGACG-CCGCGCCTTTGCGAA-GCTCCCTCGACGAGTCGAGCAGTTTGGGAATGCTGCTCTAAATGGGAGGTACATTCCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGCGATCGAAAGATGAAAAGCACTTTGGAAAGAGGGTCAAACAGCACGTGAAATTGTTGAAAGGGAAGCGCTCGTGA-CCAG-ACGCGC-GCCGTGCCGCTCCCCCGGCGTT--CTCGCTTGGGGCTCC-CGGCAC-GGCG-CGGGCCAGCGTC-GGCC-CTCGCG-GGGGGAC-AAGGGCCCAGGGAACGTGGCTC Helminthosphaeria_clavariarum_AY346283_ ---------------------------AGGAAAAGAAACCAACAGGGATTGCCCCAGTAACTGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCCGGCCCCCCCCCGC--GGGGGCCCGAGTTGTAATTTGAAGAGGATG-CTT-CGGGCGCGGC-GCCTTCCGAGTCCCCTGGAACGGGGCGCCATAGAGGGTGAGAGCCCCGTCT--GGTCGGACG-CCAAGCCCGCGTGAA-GCTCCCTCTACGAGTCGAGTAGCTTGGGAATGCTGCTCTAAGCGGGAGGTAAATGCCTTCTAAAGCTAAATACCAGCCAGAGACCGATAGCGCACAAGTAGGGTGACCGAAAGCTGAAAAGAACCTTGAAAAGAGGGTTAAAGAGCACGTGAAATTGTTGAAAGGGAAGCGCCTGCGAGCCAGAACGCGG-GCGCGGCGGATCACCCGGCGCTC-CGCGC-CGGCGCACTCCG-CCG-CGCC-CGGGCCAGCGCCGGGCC-CCGGCG-GGGGGAC-AGAGGCCCGGGGAACGTAGCTG Lasiosphaeriella_pseudobombarda_HM171286_ GCTGAACTTAAGCATATCACTAATCGGAGGAAAAGAAACCAACCGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCGGGTCCCCCCC-GCC-GGGGGCCCGAGTTGTAATTTGGAGAGGATG-CTT-CGGGCGCGGCGGCCCTCCAAGTCCCCAGGAACGGGGCGCCGCGGAGGGTGAGAGCCCCGTAC--GGTCGGCCGCCCGCGCCCGCGCGAA-GCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCCAAGCGGGAGGTACGTTCCTTCTAAAGCTAAATACCGGCCGGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACCTTGGAAAGGGGGTCAAACAGCACGTGAAATTGTTGAAAGGGAAGCGCTCGCGA-CCAG-ACGCGCGGCC-GGCCGATCCCGCGGCGCTCGCTCGC-CGCGGCGCT-CGGCCG-GACG-CGGGCCAGCGTC-GGCT-CGCGCG-GGGGGAC-GAAGGCGCGGGGAACGTGGCTC Lasiosphaeriella_noonae_daniae_HM171284_ GCTGAACTTAAGCATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCCGGCCCCC------------GCCGGAGTTGTAATTTGGAGAGGACG-CTT-CTGGCGAGGC-GCCGTCCAAGTCCCCAGGAACGGGGCGCCGCGGAGGGTGAGAGCCCCGTAC--GGTCGGACG-CCGAGCCTGTGCGAA-GCTCCCTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCAAAACGGGAGGTACGTTCCTTCTAAGGCTAAATACCGGCCGGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGGAAAGAGGGTCAAACAGCACGTGAAATTGTTGAAAGGGAAGCGCTCGTGA-CCAG-ACGCGC-GCCTCGCCGATCCGCCAGCGCTCGC-CGC-TGGCGCCCT-CGGC-GCGGCG-CGGGCCAGCGTC-GGCT-CCCGCG-GCGGGAG-AAAGGCGCCGGGAACGTGGCTC ; END; BEGIN TREES; Title ErythromadaMB; LINK Taxa = Taxa; TRANSLATE 1 Linocarpon_livistonae_DQ810207_, 2 F530, 3 Erythromada_lanciospora_DQ231442_, 4 Linocarpon_elaeidis_DQ810222_, 5 Zignoella_pulviscula_AF466091_, 6 Striatosphaeria_codinaeophora_AF178546_, 7 Lasiosphaeriella_nitida_HM171283_, 8 Camarops_ustulinoides_AY346267_, 9 Camarops_tubulina_AY346266_, 10 Leptosporella_gregaria_HM171289_, 11 Linocarpon_appendiculatum_AY346291_, 12 Caudatispora_biapiculata_AY346269_, 13 Helminthosphaeria_clavariarum_AY346283_, 14 Lasiosphaeriella_pseudobombarda_HM171286_, 15 Lasiosphaeriella_noonae_daniae_HM171284_; TREE con_50_majrule = (1:0.187043,4:0.016856,((((2:0.081879,3:0.054005)1.00:0.106909,(5:0.051157,6:0.035513)1.00:0.046956)0.56:0.017468,7:0.050008,10:0.03118,11:0.034355,(12:0.045695,(14:0.072071,15:0.035112)1.00:0.027764)1.00:0.042104,13:0.134318)0.68:0.016682,(8:0.008112,9:0.005206)1.00:0.02915)1.00:0.108054); TREE con_50_majrule = (1:0.187043,4:0.016856,((((2:0.081879,3:0.054005):0.106909,(5:0.051157,6:0.035513):0.046956):0.017468,7:0.050008,10:0.03118,11:0.034355,(12:0.045695,(14:0.072071,15:0.035112):0.027764):0.042104,13:0.134318):0.016682,(8:0.008112,9:0.005206):0.02915):0.108054); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 535; END; begin mrbayes; set autoclose = no nowarn = yes; lset nst = 6 rates = invgamma; unlink statefreq = ( all ) revmat = ( all ) shape = ( all ) pinvar = ( all ); prset applyto = ( all ) ratepr = variable; mcmcp ngen = 10000000 relburnin = yes burninfrac = 0.25 printfreq = 1000 samplefreq = 1000 nchains = 4 savebrlens = yes; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 535; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 535; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1374682453169; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 1315806582305208814; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 6208643069171584175; mqVersion 275; checksumv 0 3 2335421574 null getNumChars 535 numChars 535 getNumTaxa 15 numTaxa 15 short true bits 15 states 15 sumSquaresStatesOnly 131964.0 sumSquares 131964.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 117; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1034 635; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #1315806582305208814 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #1315806582305208814; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 917 568; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.ibeam; endTell; setActive; endTell; showWindow; getEmployee #mesquite.lists.ColorTaxon.ColorTaxon; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #1315806582305208814 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 865.1307315559534.6502614472372734598; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 917 568; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.reroot; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle on; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 1; orientRight; setCornerMode Right_Angle 50; endTell; setBackground White; setBranchColor Black; showNodeNumbers off; showBranchColors on; labelBranchLengths off; centerBrLenLabels on; showBrLensUnspecified on; showBrLenLabelsOnTerminals on; setBrLenLabelColor 0 0 255; setNumBrLenDecimals 6; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setColor Black; toggleColorPartition on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setTree '((8:0.008112,9:0.005206)1.00:0.014575,((1:0.187043,4:0.016856):0.108054,(7:0.050008,10:0.03118,11:0.034355,13:0.134318,(12:0.045695,(14:0.072071,15:0.035112)1.00:0.027764)1.00:0.042104,((2:0.081879,3:0.054005)1.00:0.106909,(5:0.051157,6:0.035513)1.00:0.046956)0.56:0.017468)0.68:0.016682)1.00:0.014575);'; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; showWindow; endTell; desuppressEPCResponse; getEmployee #mesquite.trees.ColorBranches.ColorBranches; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.ornamental.BranchNotes.BranchNotes; tell It; setAlwaysOn off; endTell; getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition; tell It; colorByPartition off; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles; tell It; setOn on; setDigits 4; writeAsPercentage off; toggleCentred on; toggleHorizontal on; toggleWhiteEdges on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocStrings.DrawTreeAssocStrings; tell It; setOn on; toggleCentred on; toggleHorizontal on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #6208643069171584175 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 917 568; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; tell It; setStateLimit 9; toggleUniformMaximum on; endTell; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges off; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleShowPaleGrid off; toggleShowPaleCellColors off; togglePaleInapplicable on; toggleShowBoldCellText off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector; tell It; autotabOff; endTell; getEmployee #mesquite.charMatrices.SelSummaryStrip.SelSummaryStrip; tell It; showStrip off; endTell; getEmployee #mesquite.align.AlignToDropped.AlignToDropped; tell It; gapCosts 8 3 2 2; subCosts 10 5 10 10 10 5 5 10 10 10 5 10; endTell; getEmployee #mesquite.molec.ColorByAA.ColorByAA; tell It; emphasizeDegeneracy off; endTell; getEmployee #mesquite.chromaseq.ColorQuality.ColorQuality; tell It; toggleAmbiguities on; toggleMarks on; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; getEmployee #mesquite.chromaseq.SourceFileInfoEditor.SourceFileInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;