#NEXUS [written Wed Jul 24 16:29:51 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=8; TAXLABELS F190 Lauriomyces_heliocephalus_FJ839659_ Lauriomyces_bellulus_FJ839658_ Bulgaria_inquinans_DQ470960_ Crinula_caliciiformis_AY544680_ Holwaya_mucida_DQ257356_ Ascocoryne_sarcoides_FJ176886_ Ascocoryne_cylichnium_EU107266_ ; END; BEGIN CHARACTERS; TITLE LauriomycesMB; DIMENSIONS NCHAR=540; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX F190 GCGGAGGAAAAGAAACCAACAGGGATTGCCTTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGC-----CTTGGCCCGAATTGTAATTTGTAGAGGATGTCTTGGGTATGG-TGCGGTCTGAGTTCCCTGGAACGGGACGCCAGAGAGGGTGAGAGCCCCGTA-CAGATCAG-TGCCTCTATCCGTGTAAGACTCCTTCGACGAGTCGAGTTGTTTGGGAATGCAGCTCAAAATGGGTGGTAAATTTCATCTAAAGCTAAATATTGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGGAAAGAGAGTTAAACAGCACGTGAAATTGTTGAAAGGGAAGCGCTCGCAATCAGACTTGCGCGTAGCTGATCATCCGGCGTTCTCGCTGGTGCACTCGGTTGCGTTCAGGCCAGCATCAGTTTTGGCGGTCGGACAAAGGCCCTAGGAATGTAGCTGTTC----GCAGTGTTATAGCCTAGGGTGCAATGCGGCCCGCTGAGACTGAG Lauriomyces_heliocephalus_FJ839659_ GCGGAGGAAAAGAAACCAACAGGGATTGCCTTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCC----TATGGTCCGAATTGTAATTTGCAGAGGATGTCTCGAGCATAG-CACGGTCTGAGTTCCCTGGAACGGGACGCCAGAGAGGGTGAGAGCCCCGTA-CAGATCAG-TGCTTCTGTTCATGTGAGACTCCTTCGACGAGTCGAGTTGTTTGGGAATGCAGCTCAAAATGGGTGGTAAATTTCATCTAAAGCTAAATATTGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGGAAAGAGAGTTAAATAGCACGTGAAATTGTTGAAAGGGAAGCGCTCGCAACCAGACTTGCGCGTAGCTGATCATCTAGCGTTCTCGCTGGTGCACTCAGTTGCGTTCAGGCCAGCATCAGTTTTGGCGGCCGGATAAAGGCCCTAGGAACGTAGCTGCTC-C-GGCAGTGTTATAGCCTAGGGTGCCATGCGGCCCGCTGAGACTGAG Lauriomyces_bellulus_FJ839658_ GCGGAGGAAAAGAAACCAACAGGGATTGCCTTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCC----TCTGGCCCGAATTGTAATTTGCAGAGGATGCTTCGAGCATAG-CACGGTCTGAGTTCCCTGGAACGGGACGCCAGAGAGGGTGAGAGCCCCGTA-CAGATCAG-TGCTTCTGTTCATGTGAGGCTCCTTCGACGAGTCGAGTTGTTTGGGAATGCAGCTCTAAATGGGTGGTAAATTTCATCTAAAGCTAAATATTGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGGAAAGAGAGTTAAATAGCACGTGAAATTGTTAAAAGGGAAGCGCTCGCAACCAGACTTGCGCGTAGCTGATCATCTAGCGTTCTCGCTGGTGCACTCAGTTACGCTCAGGCCAGCATCAGTTTTGGTGGCCGGATAAAGGCCCTAGGAACGTAGCTGCTC-C-GGCAGTGTTATAGCCTAGGGTGCCATGCGGCCCGCCGAGACTGAG Bulgaria_inquinans_DQ470960_ GCGGAGGAAAAGAAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCCCTTTCAGGGTCCGAGTTGTAATTTGTAGAGGATGTTTCGGGCGTGGCTCCGGTCTAAGTTCCTTGGAACAGGACGTCATAGAGGGTGAGAATCCCGTATGTGACTGGTAGCCTATGCCCATGTGAAACTCCTTCGACGAGTCGAGTTGTTTGGGAATGCAGCTCAAAATGGGTGGTAAATTTCATCTAAAGCTAAATATTGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGGAAAGAGAGTTAAACAGTACGTGAAATTGTTGAAAGGGAAGCGCTTGCAACCAGACTTGCACGTGGCCGATCAACCGGTGTTCTCACCGGTGCACTCGGTTGCGTTCAGGCCAGCATCGGTTTCGACGGTTGGATAAAGGCCCCGGGAATGTAGCTTCTTTCGGGGAGTGTTATAGCCCGGGGTGCAATGCAGCCTGTTGGGACCGAG Crinula_caliciiformis_AY544680_ GCGGAGGAAAAGAAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCCG---CAAGGTCCGAGTTGTAATTTGTAGAGGATGTTTCGGGTGTGG-TCCAGTCTAAGTTCCTTGGAACAGGACGTCATAGAGGGTGAGAATCCCGTATGTGACTGGGTGCCTAATCCCATGTGAAACTCCTTCAACGAGTCGAGTTGTTTGGGAATGCAGCTCAAAATGGGTGGTAAATTTCATCTAAAGCTAAATATTGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGGAAAGAGAGTTAAACAGTACGTGAAATTGTTGAAAGGGAAGCGCTTGCAACCAGACTTGCACGCAGCTGATCATCCGGTGTTCTCACCGGTGCACTCGGTTGCGTTCAGGCCAGCATCGGTTTTGGTGGTGGGATAAAGGCCCTAGGAATGTGGCTCCTCTCGGGGAGTGTTATAGCCTAGGGTGCAATGCCGCCTACCGGGACCGAG Holwaya_mucida_DQ257356_ GCGGAGGAAAAGAAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCCG---CAAGGTCCGAGTTGTAATTTGTAGAGGATGTTTCGGGTGTGG-TCCAGTCTAAGTTCCTTGGAACAGGACGTCATAGAGGGTGAGAATCCCGTATGTGACTGGGTGCCTAATCCCATGTGAAACTCCTTCAACGAGTCGAGTTGTTTGGGAATGCAGCTCAAAATGGGTGGTAAATTTCATCTAAAGCTAAATATTGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGGAAAGAGAGTTAAACAGTACGTGAAATTGTTGAAAGGGAAGCGCTTGCAACCAGACTTGCACGCAGCTGATCATCCGGTGTTCTCACCGGTGCACTCGGTTGCGTTCAGGCCAGCATCGGTTTTGGTGGTGGGATAAAGGCCCTAGGAATGTGGCTCCTCTCGGGGAGTGTTATAGCCTAGGGTGCAATGCCGCCTACCGGGACCGAG Ascocoryne_sarcoides_FJ176886_ ---------------------------------------------------------------ATTTGAAATCTGGCTCTTTCAGAGTCCGAGTTGTAATTTGTAGAAGATGCTTCGGGTGCGGCCCCAGTCTAAGTTCCTTGGAAGAGGACGTCATAGAGGGTGAGAATCCCGTATGTGACCAGGTGCCCGCGCCCATGTGAAGCTCTTTCGACGAGTCGAGTTGTTTGGGAATGCAGCTCTAAATGGGTGGTATATTTCATCTAAAGCTAAATATTGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGGAAAGAGAGTTAAACAGTACGTGAAATTGTTGAAAGGGAAGCGCTTGCAATCAGACTTGCGTGCCGTCGATCATCCCAGGTTCTCCTAGGTGCACTCGGCGGCGCTCAGGCCAGCATCGGTTCTGGTGGTGGGATAAAGGCCTTGGGAATGTAGCTCCTTTCGGGGAGTGTTATAGCCCTCGGTGCAATGCCGCCTACCGGGACCGAG Ascocoryne_cylichnium_EU107266_ -------------------CAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCTCGTTCCGAGCCCGAGTTGTAATTTGTAGAAGATGCTTCGGGTGCGGTCCCGGTCTAAGTTCCTTGGAAGAGGACGTCACAGAGGGTGAGAATCCCGTATGTGACCGGGTGCCCGCGCCTATGTGAAGCTCTTTCGACGAGTCGAGTTGTTTGGGAATGCAGCTCTAAATGGGTGGTATATTTCATCTAAAGCTAAATATTGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGGAAAGAGAGTTAAACAGTACGTGAAATTGTTGAAAGGGAAGCGCTTGCAATCAGACTTGCGCGCCGTCGATCATCCTAGGTTCTCCTGGGTGCACTCGGCGGCGTTCAGGCCAGCATCGGTTCCGGTGGTGGGATAAAGGCCTTGGGAATGTAGCTCCTCTCGGGGAGTGTTATAGCCCTCGGTGCAATGCCGCCTACTGGGACCGAG ; END; BEGIN TREES; Title LauriomycesMB; LINK Taxa = Taxa; TRANSLATE 1 F190, 2 Lauriomyces_heliocephalus_FJ839659_, 3 Lauriomyces_bellulus_FJ839658_, 4 Bulgaria_inquinans_DQ470960_, 5 Crinula_caliciiformis_AY544680_, 6 Holwaya_mucida_DQ257356_, 7 Ascocoryne_sarcoides_FJ176886_, 8 Ascocoryne_cylichnium_EU107266_; TREE con_50_majrule = (1:0.021224,(4:0.033846,((5:0.001925,6:0.001922)1.00:0.023163,(7:0.011793,8:0.024418)1.00:0.098659)0.83:0.018072)1.00:0.128418,(2:0.00377,3:0.023428)1.00:0.039845); TREE con_50_majrule = (1:0.021224,(4:0.033846,((5:0.001925,6:0.001922):0.023163,(7:0.011793,8:0.024418):0.098659):0.018072):0.128418,(2:0.00377,3:0.023428):0.039845); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 540; 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 - 540; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 540; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1374683391670; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8457492784318613288; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 7922987533356108524; mqVersion 275; checksumv 0 3 195050837 null getNumChars 540 numChars 540 getNumTaxa 8 numTaxa 8 short true bits 15 states 15 sumSquaresStatesOnly 86532.0 sumSquares 86532.0 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 1024 581; setLocation 104 107; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #8457492784318613288 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #8457492784318613288; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 907 514; setLocation 104 107; 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 #8457492784318613288 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 4619.1306587764860.6464977297990138703; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 907 514; setLocation 104 107; 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 '((7:0.011793,8:0.024418):0.0493295,((5:0.001925,6:0.001922):0.023163,(4:0.033846,(1:0.021224,(2:0.00377,3:0.023428):0.039845):0.128418):0.018072):0.0493295);'; 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 #7922987533356108524 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 907 514; setLocation 104 107; 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;