#NEXUS [written Sun Jul 21 22:57:29 GMT+00:00 2013 by Mesquite version 2.75 (build 566) at Macintosh-6.local/192.168.2.6] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=10; TAXLABELS F538 Acremonium_alcalophilum_EF543834_ Wallrothiella_subiculosa_WSU17428_ Acremonium_atrogriseum_FJ176881_ Acremonium_brachypenium_AB540496_ Acremonium_dichromosporum_AB540498_ Acremonium_murorum_Var_felina_AY283559_ Acremonium_felinum_AB540488_ Hypocrea_rufa_AY489726_ Hypocrea_schweinitzii_GU048594_ ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=496; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX F538 AAAAGAAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGG-C--TCCCTTGGGGGTCCGAGTTGTAATTTGCAGAGGATGCCTCGGGTGCGGGTTCCTTCCGAGTTCCCTGGAACGGGACGCCATAGAGGGTGAGAGCCCCGTCTGGTCGGAAACCCAGCCCGTGTGAGGCTCCCTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAG-GGGAGGTATACTCCTTCCAAGGCTAAATACCGGCTAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGAGTCAAATAGCACGTGAAATTGCTGAAAGGGAAGCGCTTATTACCAGACTTGGGTTCGGCGGTTCAACCGGCGCCACGCGCCGGGGCACTCCG--CCG-GCCCAGGCCAGCATCAGCTTTCCGTCGGGGGCAAAGGCGTCGGGAATGTAGCTCCCCCTC--GG Acremonium_alcalophilum_EF543834_ ---------------------CCTCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGG-C--TCC-TTCGGGGCCCGAGTTGTAATTTGCAGAGGATGCCTCGGGTGCGGGTTCCTTCCGAGTTCCCTGGAACGGGACGCCATAGAGGGTGAGAGCCCCGTCAGGTCGGAAACCTAGCCCGTGTGAGGCTCCCTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAG-GGGAGGTATACTCCTTCCAAAGCTAAATACCGGCTGGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGAGTCAAATAGCACGTGAAATTGTTGAAAGGGAAGCGCTCGCTACCAGACTTGGGTCC-GCGGCTCACCCGGTGCTCCGCACCGGTGCATTCCG--CGG-GCCCAGGCCAGCATCAGCTCTCCGTCAGGTTCAAAGGCTTCGGGAATGTAGCTCCCCCTC--GG Wallrothiella_subiculosa_WSU17428_ AAAAGAAACCAACAGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGG-CC-TC-------GGCCCGAGTTGTAATTTGTAGAGGATGCTTTGGGGG-AGGTGCCTTCTGAGTTCCCTGGAACGGGACGCCAGAGAGGGTGAGAGCCCCGTT--GTCGGACACCTAGCCTCTGTAAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCAAAATGGGAGGTATATCTCTTCTAAAGCTAAATATAGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGCACGTGAAATTGTTGAAAGGGAAGCGCTTGTGACCAGACTTGCGCCGGGCTGATCATCCAGTGTTCT-CACTGGTGCACTC-GACCCG-GTTCAGGCCAGCGTCGGTTCTCGCGGGGGGACAAAAGCGGTGGGAACGTAGCTC---CTCC-GG Acremonium_atrogriseum_FJ176881_ AAAAGAAACCAACAGGGATTGCCCTAGTAACGGCGAGTGAAGCGGCAACAGCTCGAATTTGAAATCTGG-CC-TC-------GGCCCGAGTTGTAATCTGTAGAGGACGCTTTTGGCG-CGGTGCCTTCCGAGTTCCCTGGAACGGGACGCCACAGAGGGTGAGAGCCCCGTAAGGTCGGACACCAAGCCTGTGTAAAGCCCCTTCGACGAGTCGAGTAGCTTGGGAATGCTGCTCTAAGCGGGAGGTATACTTCTTCTAAAGCTAAATATTGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTCAAATAGTACGTGAAATTGTTGAAAGGGAAGCGCTTGTGATCAGACTCGCGCCGGGCGGATCATCCAGTGGTCTCCACTGGTGCACTCCGG-CCG-GCGCGGGCCAGCGTCGGCTGTTGCGGGGGGACAAAAGCTCTGGGAACGTGGCTC--TCTCCGGG Acremonium_brachypenium_AB540496_ AAAAGAAACCAACAGGGATTGCCCTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGG-CC-TCAC-----GGTCCGAGTTGTAATTTGTAGAGGATGCTTCTGGCG-ACGTGCCTTCCGAGTTCCCTGGAACGGGACGCCATAGAGGGTGAGAGCCCCGTCCGGTCGTGCACCTAGCCTCTGTGAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTATACGTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGTACGTGAAATTGCTGAAAGGGAAGCGCTTATGACCAGACTTGGGCTCGGTGAATCATCCGGCGTTCT-CGCCGGTGCACTTTG--CCG-TCCCAGGCCAGCATCAGTTCGCGCCGGGGGATAAAGGCTTCGGGAATGTAGCTCC-T-TC--GG Acremonium_dichromosporum_AB540498_ AAAAGAAACCAACAGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGG-CC-TC-GT-----GCCCGAGTTGTAATTTGTAGAGGATGCTTCTGGCG-ACGCGCCTTCCGAGTTCCCTGGAACGGGACGCCATAGAGGGTGAGAGCCCCGTCCGGTCGTGCGCCTAGCCTCTGTGAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTATACGTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGTACGTGAAATTGCTGAAAGGGAAGCGCTTATGACCAGACTTGGGCGCGGCGGATCATCCGGCGTTCT-CGCCGGTGCACTCC-A-CCG-CCCCAGGCCAGCATCAGCTCGCGCCGGGGGACAAAGGCTTCGGGAATGTGGCTCCCTC----GG Acremonium_murorum_Var_felina_AY283559_ -AAAGAAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGG-CC-TC--T----GGCCCGAGTTGTAATTTGCAGAGGATGTTTCTGGCG-AGGTGCCTTCCGAGTTCCCTGGAACGGGACGCCATAGAGGGTGAGAGCCCCGTACGGTTGGTCGCTAAGCCTCTGTGAAACTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTGTACGCCTTCTAAAGCTAAATATAGGCTAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGTACGTGAAATTGTTGAAAGGGAAGCGCTCTTGACCAGACTTGCGCC-GGTTGATCATCCACCGTTCT-CGGTGGTGCACTCTG--CCG-GCTCAGGCCAGCATCAGTTCGGCTTGGGGGATAAAGGCTTCGGGAATGTGGCTC--TCTCCGGG Acremonium_felinum_AB540488_ AAAAGAAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGG-CC-TC--T----GGCCCGAGTTGTAATTTGCAGAGGATGTTTCTGGCG-AGGTGCCTTCCGAGTTCCCTGGAACGGGACGCCATAGAGGGTGAGAGCCCCGTACGGTTGGTCGCTAAGCCTCTGTGAAACTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTGTACGCCTTCTAAAGCTAAATATAGGCTAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGTACGTGAAATTGTTGAAAGGGAAGCGCTCTTGACCAGACTTGCGCC-GGTTGATCATCCACCGTTCT-CGGTGGTGCACTCTG--CCG-GCTCAGGCCAGCATCAGTTCGGCTTGGGGGATAAAGGCTTCGGGAATGTGGCTC--TCTCCGGG Hypocrea_rufa_AY489726_ -------------AGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCCCCT-AG-----GGTCCGAGTTGTAATTTGTAGAGGATGCTTTTGGTG-AGGTGCCGCCCGAGTTCCCTGGAACGGGACGCCGCAGAGGGTGAGAGCCCCGTCTGGCTGGCCACCGAGCCTCTGTAAAGCTCCTTCAACGAGTCGAGTAGTTTGGGAATGCTGCTCAAAATGGGAGGTATATGTCTTCTAAAGCTAAATATTGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACCTTGAAAAGAGGGTTAAACAGTACGTGAAATTGTTGAAAGGGAAGCGCTTGTGACCAGACTTGGGCGCGGCGGATCATCCGGGGTTCT-CCCCGGTGCACTTCG--CCGCGTTCAGGCCAGCATCAGTTCGGCGCGGGGGAAAAAGGCTTCGGGAACGTGGCTC---CTCC-GG Hypocrea_schweinitzii_GU048594_ AAAAGAAACCAACAGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGG-CCCTT--TTG--GGTCCGAGTTGTAATTTGTAGAGGATGCTTTTGGCA-AGGTGCCGCCCGAGTTCCCTGGAACGGGACGCCACAGAGGGTGAGAGCCCCGTCTGGCTGGCCACCGAGCCTCTGTAAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCAAAATGGGAGGTATATGTCTTCTAAAGCTAAATATTGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACCTTGAAAAGAGGGTTAAATAGTACGTGAAATTGTTGAAAGGGAAGCGCTTGTGACCAGACTTGGGCGCGGCGGATCATCCGGGGTTCT-CCCCGGTGCACTTCG--CCGTGTCCAGGCCAGCATCAGTTCGTCGCGGGGGAAAAAGGCTTCGGGAACGTGGCTCCC-CT---GG ; END; BEGIN TREES; Title AcremoniumMB; LINK Taxa = Taxa; TRANSLATE 1 F538, 2 Acremonium_alcalophilum_EF543834_, 3 Wallrothiella_subiculosa_WSU17428_, 4 Acremonium_atrogriseum_FJ176881_, 5 Acremonium_brachypenium_AB540496_, 6 Acremonium_dichromosporum_AB540498_, 7 Acremonium_murorum_Var_felina_AY283559_, 8 Acremonium_felinum_AB540488_, 9 Hypocrea_rufa_AY489726_, 10 Hypocrea_schweinitzii_GU048594_; TREE con_50_majrule = (1:0.030405,2:0.039856,(((3:0.040851,4:0.079381)1.00:0.053264,(7:0.002122,8:0.002171)1.00:0.075728)0.54:0.021753,(5:0.022533,6:0.014445)0.97:0.021386,(9:0.017591,10:0.006197)1.00:0.063707)1.00:0.125615); TREE con_50_majrule = (1:0.030405,2:0.039856,(((3:0.040851,4:0.079381):0.053264,(7:0.002122,8:0.002171):0.075728):0.021753,(5:0.022533,6:0.014445):0.021386,(9:0.017591,10:0.006197):0.063707):0.125615); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 496; 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 - 496; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 496; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1374447449753; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 9195792202341142429; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 2692306156899086623; mqVersion 275; checksumv 0 3 2497014532 null getNumChars 496 numChars 496 getNumTaxa 10 numTaxa 10 short true bits 15 states 15 sumSquaresStatesOnly 92659.0 sumSquares 92659.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 229; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1044 649; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #9195792202341142429 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #9195792202341142429; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 815 582; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.ibeam; endTell; 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.ManageTrees.ManageTrees; tell It; showTrees 0 #mesquite.lists.TreesList.TreesList; tell It; setTreeBlock 1; getWindow; tell It; newAssistant #mesquite.lists.NumForTreeList.NumForTreeList; tell It; suppress; setValueTask #mesquite.trees.NumberOfTaxa.NumberOfTaxa; desuppress; endTell; newAssistant #mesquite.lists.TreeListRooted.TreeListRooted; newAssistant #mesquite.lists.TreeListPolys.TreeListPolys; newAssistant #mesquite.lists.TreeListPolyAssumption.TreeListPolyAssumption; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 815 582; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; endTell; showWindow; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #9195792202341142429 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1582.1310495463696.8853029179189914605; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 815 582; 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; 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 #2692306156899086623 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 815 582; 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;