#NEXUS [written Wed Jul 24 16:49:13 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=9; TAXLABELS F524 Physalospora_zeicola_DQ377881_ Physalospora_vaccinii_FJ588249_ Acanthorhynchus_vaccinii_AY075112_ Physalospora_pyricola_DQ810230_ Physalospora_obtusa_DQ810229_ Hyponectria_buxi_AY083834_ Xylaria_acuta_AY544676_ Xylaria_hypoxylon_AY544648_ ; END; BEGIN CHARACTERS; TITLE PhysalosporaMB; DIMENSIONS NCHAR=555; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX F524 GAAACTAACAAGGA-TTCCCCTAGTAACGGCGAGTGAAGCGGGAACAGCCCAAATTTGAAAGCTGGCCGCA--A--GGTCCGCATTGTAATTTGGAGAGGATGCTTCTGGTGA-GG-T-CCTGACTGAGTCCCCTGGAACGGGGCGCCGCAGAGGGTGAGAGCCCCGTA-G-AGTCAGACGCCG-ATCCTGTGTGAAGCTCCCTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTAAATTCCTTCTAAGGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGCACGTGAAATTGCTGAAAGGGAAGCGCACGTCGCCAGACTCG-GCTTCGGTGGTAACCCGGCGTTCTCGCCGGTG-GTTCCTCCGAGGTCGGGCCAGCACCGGT----GGTTT--GGGGGCAGGAA--GCGC-AGGAACGTAGCTCCC-TC---GGGAGTGTTATAGCC----TG-CGTGGAGCGTCCCTGAGT--CACCGAGGCCCGCGGT- Physalospora_zeicola_DQ377881_ GAAACCAACAGGGA-TTGCCTTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAAGCTGGCCCTTTTAG-GGTCCGCATTGTAATTTGTAGAGGATGATTCGG-CGAGGGCT-CCTGCCTAAGTCCCCTGGAACGGGGCGTCATAGAGGGTGAGAATCCCGTATGCGGTAGGTTGCCTTAGCC-ATGTGAATCTCCTTCGACGAGTCGAGTTGTTTGGGAATGCAGCTCTAAATGGGAGGTAAATTTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGGAAAGAGAGTTAAAAAGTACGTGAAATTGTTGAAAGGGAAGCGCTTGCAACCAGACTTGTCCGCAGTTGCTCAGCCGGTCTCCTGACCGGCGTACTCTTCTGCGGCCAGGCCAGCATCAGTTCGGGCGGTC----GGAT-AAAGGCCTC-GGGAATGTGGCTCC--TCTCGGGGAGTGTTATAGCC--CGGGGTGCAATGCGGCC-AGCCTG-GACTGAGGAACTCGCT- Physalospora_vaccinii_FJ588249_ GAAACCAACAGGGA-TTGCCTCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAAGCTGGCCCCCC-AGGGGTCCGCGTTGTAATTTGCAGAGGATGCTTCGGGCGC-GG-CGCCT-TCCGAGTCCCCTGGAACGGGGCGCCATAGAGGGTGAGAGCCCCGTAT--GGTTGGACGCCT-AGCCCGTGTGAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAACGGGAGGTAAATTCCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGCACGTGAAATTGCTGAAAGGGAAGCGCCTATGACCAGACGCGCGCCGGGCGGATCATCCAGCGTTCTCGCTGGTGCACTCCGCTCGGCGCGGGCCAGCATCGGTTTCCACGGT-----GGCT-GAAG-CGCC--GGAAAGTAGCTCCCTTC--GGGGAGTGTTATAGCCGGCGTGGCG----GCACCC--GCGGG-GACCGAGGTTC-CGCG- Acanthorhynchus_vaccinii_AY075112_ ???????????GGA-TTGCCTCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAAGCTGGCCCCCC-AGGGGTCCGCGTTGTAATTTGCAGAGGATGCTTCGGGCGC-GG-CGCCT-TCCGAGTCCCCTGGAACGGGGCGCCATAGAGGGTGAGAGCCCCGTAT--GGTTGGACGCCT-AGCCCGTGTGAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAACGGGAGGTAAATTCCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGCACGTGAAATTGCTGAAAGGGAAGCGCCTATGACCAGACGCGCGCCGGGCGGATCATCCAGCGTTCTCGCTGGTGCACTCCGCCCGGCGCGGGCCAGCATCGGTTTTCGCGGT-----GGCT-GAAG-CGCC--GGAAAGTAGCTCCCTTC--GGGGAGTGTTATAGCCGGCGTGGCG----GCACCC--GCGGG-GACCGAGGTTC-CGCG- Physalospora_pyricola_DQ810230_ -------------A-TTGCCTTAGTAGCGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAAGCTGGCTCCTT-TGGGGCCCGAGTTGTAATTTGTAGAGGATGCTTTTGGTGC-GG-TGCCT-TCTGAGTCTCCTGGAAC-GGACGCCATAGAGGGTGAGAGCCCCGTAT--AGTTGGACACCA-AGCC-ATGTGAATCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCAAAATGGGAGGTAAATTTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAAAAGTACGTGAAATTGTTGAAAGGGAAGCGCTTATGACCAGACTTGTGCCCTGCGGATCAGCCGGTCTCCTGGCCGGTGTACTTCGCTTGGTTCAGGCCAGCATCAGTT----CGGTGAGGGGGATAAAAG-CCTC-AGGAACGTAGCTC--TCCTC-GGGAGTGTTATAGCC--CGGGGCAGAATACCCTC---CGGGGGACCGAGGTTCGCGCT- Physalospora_obtusa_DQ810229_ -------------A-TTGCCTTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAAGCTGGCCCTTTCAG-GGCCCGAGTTGTAATTTGTAGAGGATGCTTTTGGTGC-GG-TGCCT-TCTGAGTCCCCTGGAACGGGACGCCATAGAGGGTGAGAGCCCCGTAA--AGTTGGACACCA-AGCC-ATGTGAATCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCAAAATGGGAGGTAAATTTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAAAAGTACGTGAAATTGTTGAAAGGGAAGCGCTTATGACCAGACTTGTGCCCTGCGGATCATCCAGTCTCCTGGCCGGTGTACTTCGCTGGGCCCAGGCCAGCATCAGTT----CGGTGAGGGGGATAAAAG-CCTC-AGGAATGTAGCTC--TCCTC-GGGAGTGTTATAGCC--TGTTGCAGAATACCGCC-AGGGG--GACCGAGGTTCGCGCT- Hyponectria_buxi_AY083834_ GAACCCAACAGGGAATTCCC-CAATAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCCCCC--G--GGTCCGAGTTGTAATTTGTAGAGGATGCTTTTGGCGC-GG-CGCCT-TCCGAGTTCCCTGGAACGGGACGCCTTAGAGGGTGAGAGCCCCGTA--CGGTTGGACGCCT-AGCCTCTGTAAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTAAATTTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGCACGTGAAATTGTTGAAAGGGAAGGACTTATGACCAGACTTTTGCCTTGGGGATCATCCGGTGTTCTCACCGGTGCACTTCGCTTGGCTTAGGCCAGCATCGGTTT---CTGTG-GGGGGACAAAAG--CTCCGGGAACGTAGCTCC-TT-T--GGGAGTGTTATAGCC--CTCTGCATAATACCCCCGTGGG---GACCGAGGTTCGCGCT- Xylaria_acuta_AY544676_ ----CCAACAGGGA-TTGCCCTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCCTTC--G--GGTCCGAGTTGTAATTTGTAGAGGATGCTTTTGGCGC-GG-TGCCT-TCCGAGTTCCCTGGAACGGGACGCCTTAGAGGGTGAGAGCCCCGTA--CGGTTGGACACTA-AGCCTCTGTAAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTAAATTTCTTCTAAAGCTAAATATTGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGCACGTGAAATTGTTGAAAGGGAAGCGTTTGCGACCAGACCTTTTCCTAGCGGATCATCCGGTGTTTTCACCGGTGCACTTCGCTAGGTTTAGGCCAGCATCGGTTTCC---GT-AGGGGGATAAAAG--CTCTGGGAACGTAGCTCC-TCC---GGGAGTGTTATAGCC--CTCTGCATAATACCCTT-ACAGG--GACCGAGGACCGCGCT- Xylaria_hypoxylon_AY544648_ GAAACCAACAGGGA-TTGCCCTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCTTTC--G--GGTCCGAGTTGTAATTTGTAGAGGATGCTTTTGGCGC-GG-TGCCT-TCCGAGTTCCCTGGAACGGGACGCCTTACAGGGTGAGAGCCCCGTA--CGGTTGGACACCA-AGCCTCTGTAAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTAAATTTCTTCTAAAGCTAAATATTGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGCACGTGAAATTGTTGAAAGGGAAGCGTTTGCGACCAGACCTTTTCTTAGCGGATCATCCGGTGTTATCACCGGTGCACTTCGCTAAGTTTAGGCCAGCATCGGTTTC---TGT-AGGGGGATAAAAG-CCTT-GGGAACGTAGCTCC-TTC---GGGAGTGTTATAGCC--CTTTGCATAATACCCTTCTGGG---GACCGAGGACCGCGCTA ; END; BEGIN TREES; Title PhysalosporaMB; LINK Taxa = Taxa; TRANSLATE 1 F524, 2 Physalospora_zeicola_DQ377881_, 3 Physalospora_vaccinii_FJ588249_, 4 Acanthorhynchus_vaccinii_AY075112_, 5 Physalospora_pyricola_DQ810230_, 6 Physalospora_obtusa_DQ810229_, 7 Hyponectria_buxi_AY083834_, 8 Xylaria_acuta_AY544676_, 9 Xylaria_hypoxylon_AY544648_; TREE con_50_majrule = (1:0.207418,(3:0.005309,4:0.005042)1.00:0.051913,((2:0.180019,(5:0.021546,6:0.018069)0.53:0.017011)1.00:0.047297,(7:0.028132,(8:0.012676,9:0.016167)1.00:0.044247)1.00:0.041093)1.00:0.054548); TREE con_50_majrule = (1:0.207418,(3:0.005309,4:0.005042):0.051913,((2:0.180019,(5:0.021546,6:0.018069):0.017011):0.047297,(7:0.028132,(8:0.012676,9:0.016167):0.044247):0.041093):0.054548); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 555; END; begin mrbayes; set autoclose = no nowarn = yes; lset nst = 6 rates = gamma; 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 - 555; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 555; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1374684553637; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 3533476311537349641; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 197172343000369305; mqVersion 275; checksumv 0 3 251240853 null getNumChars 555 numChars 555 getNumTaxa 9 numTaxa 9 short true bits 15 states 15 sumSquaresStatesOnly 94354.0 sumSquares 94354.0 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 1111 672; setLocation 104 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #3533476311537349641 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #3533476311537349641; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 994 605; setLocation 104 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 #3533476311537349641 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 865.1307281883277.6637910107867453330; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 994 605; setLocation 104 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 off; 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 2; setTree '((8:0.012676,9:0.016167):0.0221235,(7:0.028132,((1:0.207418,(3:0.005309,4:0.005042):0.051913):0.054548,(2:0.180019,(5:0.021546,6:0.018069):0.017011):0.047297):0.041093):0.0221235);'; 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 #197172343000369305 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 994 605; setLocation 104 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;