#NEXUS [written Wed Jul 24 15:58:22 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=7; TAXLABELS F161 Camarosporium_brabeji_EU552105_ Microdiplodia_hawaiiensis_DQ885897_ Camarosporium_mamanes_DQ885900_ Camarosporium_leucadendri_EU552106_ Saccharata_kirstenboschensis_FJ372392_ Saccharata_proteae_FJ150707_ ; END; BEGIN CHARACTERS; TITLE CamarosporiumMB; DIMENSIONS NCHAR=1170; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX F161 GCGTCTTCTGGCGCCCTCTCT-CCCGGGTGGTAGAGGTAAAACTCTCACGCGG-CACATGTCTGAATCC--TTTTTTTACGAGC-ACCTT---T-G---------------TTCTCCTT---CGG-T--------GGGGC---AACCTG-CCGTTGG-A-CCCATCAAAAC----TCT--CTT-------TGCA-TCT-AGCATTACCTGTTCTGA--TA-CCAACAAT-AGTTACAaCTTTCAACAATGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCATGGGGCATGCCTGTTCGAGCGTCATCTACACCC-TCAAGCTCTGCTTGGTGTTGGGCGTCTGTCCCGCCTATGTGCGTGGA-CTCGCCCTAAATCTATTGGCAGCGGTCCTTGCCT-CCTCTC--GCGCAGCACATT-----GCGCTTCTTGAGGTGTGCG-----GCCCGCGTCCACGAAGC-AACATTACC---GT-----CTTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCCTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCTCTCTCTGAGGGTCCGAGTTGTAATTTGCAGAGGATGCTTTGGCATTGGCGGCGGTCTAAGTTCCTTGGAACAGGACATCGCAGAGGGTGAGAATCCCGTACGTGGGCGCCTGCCTTTGCCGTGTAAAGCTCCTTCGACGAGTCGAGTTGTTTGGGAATGCAGCTCTAAATGGGAGGTAAATTTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGTACTTTGGAAAGAGAGTCAAAAAGCACGTGAAATTGTTGAAAGGGAAGCGCTTGCAGCCAGACTTGCCCGCAGTTGCTCACCTAGGCTTTGGCCTGGGGCACTCTTCTGCGGGCAGGCCAGCATCAGTTTGGGCGGTTGGATAAAGGCCTCTATCACGTATCTCCCTTCGGGGTGACCTTATAGGGGAGGCGTAACGCGACCAGCCCGGACTGAGGTCCGCGC Camarosporium_brabeji_EU552105_ GCGGCCCCCGGCGG-AAGTGTCCCCGGGCGGTAGAGGTAACACTCTCACGCGGCCACATGCCTTCATCC-TTTTTTTTACGAGC-ACCTT---TCG---------------TTCTCCTT---CGG-T--------GGGGC---AACCTG-CCGTTGGAA-CCTATCAAAAC-C--TTT--TTT-------TGCA-TTT-AGCATTACCTGTTCTGA--TA-CAAACAAT-CGTTACAaCTTTCAACAATGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCATGGGGCATGCCTGTTCGAGCGTCATCTACACCC-TCAAGCTCTGCTTGGTGTTGGGCGTCTGTCCCGCCTCTGCGCGCGGA-CTCGCCCCAAATTCATTGGCAGCGGTCCTTGCCT-CCTCTC--GCGCAGCACATT-----GCGCTTCTCGAGGTGCGCG-----GGCCGCGTCCACGAAGC-AACATTACC---GT-----CTTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCCTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCTCTCTTTGGGGGTCCGAGTTGTAATTTGCAGAGGATGCTTTGGCATTGGCGGCGGTCTAAGTTCCTTGGAACAGGACATCGCAGAGGGTGAGAATCCCGTACGTGGGCGCCTGCCTTTGCCGTGTAAAGCTCCTTCGACGAGTCGAGTTGTTTGGGAATGCAGCTCTAAATGGGAGGTAAATTTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGTACTTTGGAAAGAGAGTCAAAAAGCACGTGAAATTGTTGAAAGGGAAGCGCTTGCAGCCAGACTTGCCCGCAGTTGCTCACCTAGGCTTTGGCCTGGGGCACTCTTCTGCGGGCAGGCCAGCATCAGTTTGGGCGGTTGGATAAAGGCCTCTGTCACGTATCTTCCTTCGGGATGACCTTATAGGGGAGGCGTAATGCAACCAGCCCGGACTGAGGTCCGCGC Microdiplodia_hawaiiensis_DQ885897_ GCGGCCTCCGGGGGTAACTC-CCCCGGGTGGTAGAGGTAACACTCGCACGCT-CCACATGCCTTAATCC--TTTTTTTACGAGC-ACCTT---TCG---------------TTCTCCTT---CGG-T--------GGGGC---AACCTG-CCGTTGGAA-CCCATCAAAAA-CCC-TT--TTT-------TGCA-TCT-AGCATTACCTGTTCCGA--TA-CAAACAAT-CGTTACAaCTTTCAACAATGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCATGGGGCATGCCTGTTCGAGCGTCATCTACACCC-TCAAGCTCTGCTTGGTGTTGGGCGTCTGTCCCGCCTCTGCGCGCGGA-CTCGCCCCAAATTCATTGGCAGCGGTCCTTGCCC-C-TCTC--GCGCAGCACATT-----GCGCTTCTCGAGGGGCGCG-----GCCCGCGTCCACGAAGCAAACATTACC---GT-----CTTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCCTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCTCTCTTTGGGGGTCCGAGTTGTAATTTGCAGAGGATGCTTTGGCATTGGCGGCGGTCTAAGTTCCTTGGAACAGGACATCGCAGAGGGTGAGAATCCCGTACGTGGGCGCCTGCCTTTGCCGTGTAAAGCTCCTTCGACGAGTCGAGTTGTTTGGGAATGCAGCTCTAAATGGGAGGTAAATTTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGTACTTTGGAAAGAGAGTCAAAAAGCACGTGAAATTGTTGAAAGGGAAGCGCTTGCAGCCAGACTTGCCCGCAGTTGCTCACCTAGGCTTTGGCCTGGGGCACTCTTCTGCGGGCAGGCCAGCATCAGTTTGGGCGGTTGGATAAAGGCCTCTGTCACGTATCTTCCTTCGGGATGACCTTATAGGGGAGGCGTAATGCAACCAGCCCGGACTGAGGTCCGCGC Camarosporium_mamanes_DQ885900_ GCGGCCCCTGG---TAACCCCGGGCGG----TAGAGGTAACACTCGCACGCG-CCACATGCCCTAATCC--TTTTTTTACGAGC-ACCTT---TCG---------------TTCTCCTT---CGG-T--------GGGGC---AACCTG-CCGCTGGAA-CTTATCAAAAC-CCTTTT--TTT-------TGCA-TCT-AGCATTACCTGTTCTGA--TA-CAAACAAT-CGTTACAaCTTTCAACAATGGATCTCTTGGCTCTGGCATCGATGAAGAACGCACCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGTGGGGCATGCCTGTTCGAGCGTCATCTACACAC-TCAAGCTCTGCTTGGTGTTGGGCGTCTGTCCCGCCTCTGCGCGCGGA-CTCGCCCCAAATTCATTGGCAGCGGTCCTTGCCC-CCTCTC--GCGCAGCACATT-----GCGCTTCTCGAGGGGCGCG-----GCCCGCGTCCACGAAGCAAACATTACC---GT-----CTTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAGAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Camarosporium_leucadendri_EU552106_ GCGGCCCCTGG---TAACCCCGGGCGG----TAGAGGTAACACTCGCACGCG-CCACATGCCTTAATCC--TTTTTTTACGAGC-ACCTT---TCG---------------TTCTCCTT---CGG-T--------GGGGC---AACCTG-CCGCTGGAA-CTTATCAAAAA-CC-TTT--TTT-------TGCA-TCT-AGCATTACCTGTTCTGA--TA-CAAACAAT-CGTTACAaCTTTCAACAATGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGTGGGGCATGCCTGTTCGAGCGTCATCTACACCC-TCAAGCTCTGCTTGGTGTTGGGCGTCTGTCCCGCCTCTGCGCGCGGA-CTCGCCCCAAATTCATTGGCAGCGGTCCTTGCCC-CCTCTC--GCGCAGCACATT-----GCGCTTCTCGAGGGGCGCG-----GCCCGCGTCCACGAAGCAAACATTACC---GT-----CTTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCCTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCTCTCTTTGGGGGTCCGAGTTGTAATTTGCAGAGGATGCTTTGGCATTGGCGGCGGTCTAAGTTCCTTGGAACAGGACATCGCAGAGGGTGAGAATCCCGTACGTGGGCGCCTGCCTTTGCCGTGTAAAGCTCCTTCGACGAGTCGAGTTGTTTGGGAATGCAGCTCTAAATGGGAGGTAAATTTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGTACTTTGGAAAGAGAGTCAAAAAGCACGTGAAATTGTTGAAAGGGAAGCGCTTGCAGCCAGACTTGCCCGCAGTTGCTCACCTAGGCTTTGGCCTGGGGCACTCTTCTGCGGGCAGGCCAGCATCAGTTTGGGCGGTTGGATAAAGGCCTCTGTCACGTATCTTCCTTCGGGATGACCTTATAGGGGAGGCGTAATGCAACCAGCCCGGACTGAGGTCCGCGC Saccharata_kirstenboschensis_FJ372392_ -------------------------------ACGAGTTCTGGGTCCTTCGGGGCCCG-TCCTCCAACCC--TTTGTCTACAAACCACGTTGCTTCGGCGGGCAGCCGGGG-TCCGCCTCGCGCGG-TTCC------GGGT---CA-CTGCCCGCCGGAGGATTACCACAAA-CCC-TTGCTTTAAAACAATGCAGTCTGACCGAA-------------TATCAAATATT-C--TAAAaCTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGAGGGGCATGCCTGTTCGAGCGTCAT-TACACCCCTCAAGCACTGCTTGGTATTGGGCCCC-GTCC----TCACCGGGCGGGCCTT-----AAAGACCT---CGGCGG-CGGCGCCGTAGCCTCAAGCGTAGTAATTCTTTC-TCGCTT-TGGAGG-CCGCGGCGTCTCCCGCC-GGACGAACCTTT--TTAC-TTTCTATCAAGGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAATAAGCGGAG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Saccharata_proteae_FJ150707_ -------------------------------ACGAGTTCTGGGTCCTTCGGGGCCCG-TCCTCCAACCC--TTTGTCTACAAACCACGTTGCTTCGGCGGGCAGCCGGGGGTCCGCCCCGCGCGGCTTCCCCCC--GGGT--CCA-CTGCCCGCCGGAGGATTACCACAAAACCC-TTGCTTTAAAACAATGCAGTCTGACCGAA-------------TATCAAATATT-C--TAAAaCTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGAGGGGCATGCCTGTTCGAGCGTCAT-TACACCCCTCAAGCACTGCTTGGTATTGGGCCCC-GTCC----TCACCGGGCGGGCCTT-----AAAGACCT---CGGCGG-CGGCGTCGTAGCCTCAAGCGTAGTAATTCTTTC-TCGCTT-TGGAGG-CCGCGGCGTCTCCCGCC-GGACGAACCTTT--TTACCATTCTATCAAGGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAGAAACCAACAGG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ; END; BEGIN TREES; Title CamarosporiumMB; LINK Taxa = Taxa; TRANSLATE 1 F161, 2 Camarosporium_brabeji_EU552105_, 3 Microdiplodia_hawaiiensis_DQ885897_, 4 Camarosporium_mamanes_DQ885900_, 5 Camarosporium_leucadendri_EU552106_, 6 Saccharata_kirstenboschensis_FJ372392_, 7 Saccharata_proteae_FJ150707_; TREE con_50_majrule = (1:0.029256,2:0.00727,(3:0.004469,((4:0.009503,5:9.41E-4)0.59:0.003864,(6:0.002675,7:0.006136)1.00:0.198438)0.99:0.00903)1.00:0.005599); TREE con_50_majrule = (1:0.029256,2:0.00727,(3:0.004469,((4:0.009503,5:9.41E-4):0.003864,(6:0.002675,7:0.006136):0.198438):0.00903):0.005599); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 1170; 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 - 1170; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 1170; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1374681502650; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 7004442939203592648; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 7587950953688643410; mqVersion 275; checksumv 0 3 1265891497 null getNumChars 1170 numChars 1170 getNumTaxa 7 numTaxa 7 short true bits 1152921504606846991 states 15 sumSquaresStatesOnly 125769.0 sumSquares 1.6140901064495884E19 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 1208 658; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #7004442939203592648 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #7004442939203592648; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1091 591; 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 #7004442939203592648 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 865.1305672533655.1791734517591979453; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1091 591; 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 '((6:0.002675,7:0.006136)1.00:0.099219,((4:0.009503,5:9.41E-4)0.59:0.003864,(3:0.004469,(1:0.029256,2:0.00727):0.005599)1.00:0.00903)0.99:0.099219);'; 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 #7587950953688643410 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1091 591; 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;