#NEXUS [written Wed Jul 24 16:58:37 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=13; TAXLABELS Bionectria_pityrodes_AF210672_ Bionectria_coronata_AF210667_ Stilbocrea_macrostoma_AY489725_ Acremonium_tubakii_AY305033_ Acremonium_hansfordii_FJ765369_ Verticillium_insectorum_HQ248107_ F388 Acremonium_potronii_AB470542 Geosmithia_putterillii_AB047215_ Geosmithia_lavendula_D88325_ Acremonium_alternatum_FJ176883_ Mycoarachis_inversa_GQ505991_ Acremonium_chrysogenum_AY228563_ ; END; BEGIN CHARACTERS; TITLE VerticilliumMB; DIMENSIONS NCHAR=550; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Bionectria_pityrodes_AF210672_ TATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCCTAGTAACGGCGAGTGAAGCGGCAACAGGCTCAAATTTGAAATCT-GGC-CCTAG--GCCCGAGTTGTAATTTGTAGAGGATGTTTCTGGCGAAGTGCCTTCCGAGTTCCCTGGAACGGGACGCCATAGAGGGTGAGAGCCCCGTACGGTTGGATGCCTAGCCTCTGTGAAACTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTATACGTCTTCTAAAGCTAAATATTGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGTACGTGAAATTGTTGAAAGGGAAGCGGTTATGACCAGACTTGGA-CAGGTTGATCATCCACGGTTCTCTGTGGTGCACTCTGCCTGTCCAGGCCAGCATCAGTTCGCTTCGGGGGATAAAGACTTTGGGAATGTGGCTCCCTCG-GGAGTGTTATAGCCCATTGTGCAATACCCTGATCCGGACTGAGGTTCGCG Bionectria_coronata_AF210667_ TATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCCTAGTAACGGCGAGTGAAGCGGCAACA-GCTCAAATTTGAAATCT-GGC-CCTAG--GCCCGAGTTGTAATTTGTAGAGGATGTTTCTGGCGACGTGTCTTCCGAGTTCCCTGGAACGGGACGCCATAGAGGGTGAGAGCCCCGTACGGTTGATTACCTAGCCTCTGTGAAACTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTATACGTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGTACGTGAAATTGTTGAAAGGGAAGCGTTTATGACCAGACTTGAG-TAGGTTGATCATCCGTGGTTCTCCGCGGTGCACTCTGCCTGCTCAGGCCAGCATCAGTTCGCTTTGGGGGATAAAAGCTTCGGGAATGTGGCTCCCTCG-GGAGTGTTATAGACCGTTGCATAATACCCTGGAGCGGACTGAGGTTCGCG Stilbocrea_macrostoma_AY489725_ ------------------------------------GCCCTAGTAACGGCGAGTGAAGCGGCAACA-GCTCAAATTTGAAATCT-GGC-CCTAG--GCCCGAGTTGTAATTTGTAGAGGATGTTTCTGGTGCGGTGCCTTCCGAGTTCCCTGGAACGGGACGCCATAGAGGGTGAGAGCCCCGTCCGGTCGTGCGCTAAGCCTATGTGAAACTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTATACGTCTTCTAAAGCTAAATATTGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGTACGTGAAATTGCTGAAAGGGAAGCGCTTATGACCAGACTTGGGCTAGGTGAATCATCCGGCGTTCTCGCCGGTGCACTTTGCCTGCCCAGGCCAGCATCAGTTCACGTCGGGGGACAAAGGCGTCGGGAATGTGGCTCCCTCG-GGAGTGTTATAGCCCGGCGTGTAATGCCCTGGCGAGGACTGAGGTACGCG Acremonium_tubakii_AY305033_ ---------------------------------------------------------------------------------------------------------------------------------------GCCTTCT?AGTTCCCTGGAACGGG?C?CCATAGAGGGTGAGAG?CCCGTCCGGT?GTGCGCCTAGCC?CTGTAAAGCTCC?TC??CGAGTT?AGTAGTTTGGGAATGCT?CTCT?AATGGGAGGTATACGTCTTCTA?AG?TAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCCCTTTGAAAAGAGGGTTAAATAGTACGTGAAATTGCTGAAAGGGAAGCGCTTATGACCAGACTTGGGCGCGGCGGATCATCCGGCGTTCTCGCCGGTGCACTCCACCGCCCCAGGCCAGCATCAGTTCGCGCCGGGGGATAAAGGCTTCGGGAATGTGGCTCTCTCG-GGAGTGTTATAGCCCGCTGCGTAATACCCTGGCGCGGACTGAGGTCCGCG Acremonium_hansfordii_FJ765369_ TATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCCTAGTAACGGCGAGTGAAGCGGCAACA-GCTCAAATTTGAAATCT-GGC-TCTCGG-GCCCGAGTTGTAATTTGTAGAGGATGTTTCTGGCGACGTGTCTTCCGAGTTCCCTGGAACGGGACGCCATAGAGGGTGAGAGCCCCGTCCGGTCGTACGCCTAGCCTCTGTGAAACTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCAAAATGGGAGGTATACGTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGTACGTGAAATTGCTGAAAGGGAAGCGCTCATGACCAGACTTGGGCTCGGTGAATCATCCGGCGTTCTCGCCGGTGCACTTTGCCGGCCCAGGCCAGCATCAGCTCGCCTCGGGGGATAAAGGCTTCGGGAATGTAGCTCCCTCGTGGAGTGTTATAGACCGTTGCGTAATACCCTGGGGCGGGCTGAGGTACGCG Verticillium_insectorum_HQ248107_ --------------------------------------------AACGGCGAGTGAAGCGGCAACA-GCTCAAATTTGAAATCTTGGC-CCCAG--GCCCGAATTGTAATTTGCAGAGGATGTTTCTGGCGACGCGCCTTCCGAGTTCCTTGGAACAGGACGCCAAAGAGGGTGAGAGCCCCGTCCGGTCGTGCGCCTAGCCTATGTGAAACTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTATACGTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGTACGTGAAATTGCTGAAAGGGAAGCGCTTATGACCAGACTTGGG-GCGGTTAATCATCCGGCGTTCTCGCCGGTGCACTTTGCCGTCCCAGGCCAGCATCAGTTTGCTTCGGGGGATAAAGGCTTCGGGAATGTGGCTCCCTCG-GGAGTGTTATAGCCCGTTGTGTAATACCCTGGAGCGGACTGAGGTACGCG F388 TATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACA-GCTCAAATTTGAAATCT-GGC-CCTAG--GCCCGAATTGTAATTTGCAGAGGATGCTTCTGGCGACGCGCCTTCCGAGTTCCTTGGAACAGGACGCCAAAGAGGGTGAGAGCCCCGTCCGGTCGTGCGCCTAGCCTCTGTGAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTATACGTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGTACGTGAAATTGCTGAAAGGGAAGCGCTTATGACCAGACTTGGG-TCGGTTAATCACCCGGCGTTCTCGCCGGTGCACTTGGCCGGCCCAGGCCAGCATCAGTTTGCTTCGGGGGATAAAGGTTTCGGGAATGTGGCTCCCTCG-GGAGTGTTATAGCCCGTTGCGTAATACCCTGGAGCGGACTGAGGTACGCG Acremonium_potronii_AB470542 -------------------------------------------------CGAGTGAAGCGGCAACA-GCTCAAATTTGAAATCT-GGC-ACTTGGTGCCCGAGTTGTAATTTGTAGAGGATGCTTTTGGCGACGCGCCTTCCGAGTTCCCTGGAACGGGACGCCATAGAGGGTGAGAGCCCCGTCCGGTCGTGCGCCTAGCCTCTGTAAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTATACGTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGTACGTGAAATTGCTGAAAGGGAAGCGCTTATGACCAGACTTGGGCGCGGCGGATCATCCGGCGTTCTCGCCGGTGCACTCCACCGCCCCAGGCCAGCATCAGTTCGCGCCGGGGGACAAAGGCTTCGGGAATGTGGCTCCCTCG-GGAGTGTTATAGCCCGTTGCGTAATACCCTGGTGCGGACTGAGGTCCGCG Geosmithia_putterillii_AB047215_ TATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCTTAGTAACGGCGAGTGAAGCGGCAACA-GCTCAAATTTGAAATCT-GGCCCCCAG--GCCCGAGTTGTAATTTGTAGAGGATGCTTCTGGCGACGCGCCTTCCGAGTTCCCTGGAACGGGACGCCAAAGAGGGTGAGAGCCCCGTCCGGTCGTGCGCCTAGCCTCTGTGAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTATACGTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGTACGTGAAATTGCTGAAAGGGAAGCGCTTATGACCAGACTTGGGCTTGGTGAATCATCCGGCGTTCTCGCCGGTGCACTTTGCCGGTCCAGGCCAGCATCAGTTCGTCCCGGGGGATAAAGGCTTCGGGAACGTAGCTCTTTCG-GGAGTGTTATAGACCGTTGCGTAATACCCTGGGGTGGACTGAGGTACGCG Geosmithia_lavendula_D88325_ TATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAACA-GCTCAAATTTGAAATCT-GGCCCCCAG--GCCCGAGTTGTAATTTGTAGAGGATGATTCTGGCGACGCGCCTTCCGAGTTCCCTGGAACGGGACGCCATAGAGGGTGAGAGCCCCGTCCGGTCGTGCGCCTAGCCTCTGTGAATCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTATACGTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAAAAGTACGTGAAATTGCTGAAAGGGAAGCGCTTATGACCAGACTTGGGCGTGGTGAATCATCCGGCGTTCTCGCCGGTGCACTTTGCCTGTCCAGGCCAGCATCAGTTCTCCCCGGGGGATAAAGGCTTCGGGAATGTAGCTCCTTCG-GGAGTGTTATAGACCGTTGCGTAATACCCTGGGGGGGACTGAGGTACGCG Acremonium_alternatum_FJ176883_ TATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCCTAGTAACGGCGAGTGAAGCGGCAACA-GCTCAAATTTGAAATCT-GGCCTCACG--GTCCGAGTTGTAATTTGTAGAGGATGCTTCTGGCGACGTGCCTTCCGAGTTCCCTGGAACGGGACGCCATAGAGGGTGAGAGCCCCGTCCGGTCGTGCACCTAGCCTCTGTGAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTATACGTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGTACGTGAAATTGCTGAAAGGGAAGCGCTTATGACCAGACTTGGGCTCGGTGAATCATCCGGCGTTCTCGCCGGTGCACTTTGCCGTCCCAGGCCAGCATCAGTTCGCGCCGGGGGATAAAGGTTTCGGGAACGTGGCTCCCTCG-GGAGTGTTATAGCCCGTTGCGTAATACCCTGGCGTGGACTGAGGTCCGCG Mycoarachis_inversa_GQ505991_ ----------CGGAGGAAAAGAAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAACA-GCTCAAATTTGAAATCT-GGCCCCCCG--GCCCGAGTTGTAATTTGCAGAGGATGCTTCTGGCGACGTGCCTTCCGAGTTCCCTGGAACGGGACGCCATAGAGGGTGAGAGCCCCGTCCGGTTGTGCGCCTAGCCTCTGTGAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTATACGTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGTACGTGAAATTGCTGAAAGGGAAGCGCTTATGACCAGACTTGGGCCCGGTGAATCATCCAGCGTTCTCGCTGGTGCACTTTGCCGGCCCAGGCCAGCATCAGTTCGCGCCGGGGGATAAAGGCTTCGGGAATGTAGCTCCCTCG-GGAGTGTTATAGACCGTTGCGCAATACCCTGGCGCGGACTGAGGTACGCG Acremonium_chrysogenum_AY228563_ ---------------------------------------------ACGGCGAGTGAAGCGGCAACA-GCTCAAATTTGAAATCT-GGCCCCCCG--GCCCGAGTTGTAATTTGCAGAGGATGCTTCTGGCGACGCGCCTTCCGAGTTCCCTGGAACGGGACGCCACAGAGGGTGAGAGCCCCGTCCGGTCGTGCGCCTAGCCTGTGTGAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTATACGTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGTACGTGAAATTGCTGAAAGGGAAGCGCTTATGACCAGACTTGGGCCCGGTGAATCA-CCAGCGTTCTCGCTGGTGCACTTTGCCGGCCCAGGCCAGCATCAGTTCGCGCCGGGGGATAAA--------------------------------------------------------------------------- ; END; BEGIN TREES; Title VerticilliumMB; LINK Taxa = Taxa; TRANSLATE 1 Bionectria_pityrodes_AF210672_, 2 Bionectria_coronata_AF210667_, 3 Stilbocrea_macrostoma_AY489725_, 4 Acremonium_tubakii_AY305033_, 5 Acremonium_hansfordii_FJ765369_, 6 Verticillium_insectorum_HQ248107_, 7 F388, 8 Acremonium_potronii_AB470542, 9 Geosmithia_putterillii_AB047215_, 10 Geosmithia_lavendula_D88325_, 11 Acremonium_alternatum_FJ176883_, 12 Mycoarachis_inversa_GQ505991_, 13 Acremonium_chrysogenum_AY228563_; TREE con_50_majrule = (1:0.053844,2:0.02833,(3:0.056022,(((4:0.018623,8:0.007766)1.00:0.032692,11:0.018687)0.92:0.009938,((5:0.028426,(9:0.012004,10:0.021798)1.00:0.017457)0.64:0.008595,(12:0.0069,13:0.011605)1.00:0.017885)0.63:0.008945)0.66:0.00914,(6:0.016286,7:0.012086)1.00:0.023756)1.00:0.053185); TREE con_50_majrule = (1:0.053844,2:0.02833,(3:0.056022,(((4:0.018623,8:0.007766):0.032692,11:0.018687):0.009938,((5:0.028426,(9:0.012004,10:0.021798):0.017457):0.008595,(12:0.0069,13:0.011605):0.017885):0.008945):0.00914,(6:0.016286,7:0.012086):0.023756):0.053185); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 550; 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 - 550; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 550; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1374685117655; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 1292897901767241425; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 8275988875858474072; mqVersion 275; checksumv 0 3 3621520605 null getNumChars 550 numChars 550 getNumTaxa 13 numTaxa 13 short true bits 15 states 15 sumSquaresStatesOnly 133111.0 sumSquares 133111.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 88; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 712 607; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #1292897901767241425 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #1292897901767241425; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 624 540; 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 #1292897901767241425 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1205.1312964298897.3952784494062085396; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 624 540; 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 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 '((9:0.012004,10:0.021798):0.0087285,(5:0.028426,((12:0.0069,13:0.011605):0.017885,((11:0.018687,(4:0.018623,8:0.007766):0.032692):0.009938,(3:0.056022,(1:0.053844,2:0.02833):0.053185,(6:0.016286,7:0.012086):0.023756):0.00914):0.008945):0.008595):0.0087285);'; 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 #8275988875858474072 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 624 540; 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;