#NEXUS [written Wed Jul 24 16:38:30 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=11; TAXLABELS Chaetomium_globosum_AY346272_ Chaetomium_microascoides_AY346273_ F504 Ophioceras_tenuisporum_AY346295_ F520 Buergenerula_spartinae_DQ341492_ Magnaporthe_salvinii_DQ341498_ Muraeriata_collapsa_EU527996_ Muraeriata_africana_EU527995_ Gaeumannomyces_medullaris_FJ176854_ Gaeumannomyces_cylindrosporus_DQ341494_ ; END; BEGIN CHARACTERS; TITLE MagnaporthaceaeMB; DIMENSIONS NCHAR=569; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Chaetomium_globosum_AY346272_ AAAAGAAACCAACAGGGATTGCCCTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGC-----TTC------GGCCCGAGTTGTAATTTGCAGAGGAAGCTTTAGGCG-CGGCACTTTCTGAGTCCCCTGGAACGGGGCGCCATAGAGGGTGAGAGCCCCGTATAGTTAGATGCCTAGCCTGTGTAAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCAAAATGGGAGGTAAATTTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGCACGTGAAATTGTTGAAAGGGAAGCGCTTGTGACCAGACT-TGCGCCGGGCAGATC-ATCCGGTG-----TTCT-CACC-GGTGCACTCTG-CCC-GG--CTCAGGCCAGCATCGGTTCTCGCGGGGGGATAAAGG-CCCTGGGAACGTAG-CTCCTCC----GGGA-GTGTTATAGCC-CG-GGGCGTAATGCCCTCG--------CGGGGA--CCGAGGTTC Chaetomium_microascoides_AY346273_ AAAAGAAACCAACAGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGC-----CTC------GGCCCGAGTTGTAATTTGCAGAGGAAGCTTTAGGCG-CGGCACCAACTGAGTCCCCTGGAACGGGGCGCCATAGAGGGTGAGAGCCCCGTATAGTTGGACGCCTAGCCTGTGTAAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCAAAATGGGAGGTAAATTTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGCACGTGAAATTGTTGAAAGGGAAGCGCTTGTGACCAGACT-TGCGCCGGGCCGATC-ATCCGGTG-----TTCT-CACC-GGTGCACTCGG-CCC-GG--CTCAGGCCAGCATCGGTTCTCGTGGGGGGATAAAGG-TCCCGGGAACGTAG-CTCCTCC----GGGA-GTGTTATAGCC-CG-GGGCGTAATGCCCTCG--------CGGGGA--CCGAGGTTC F504 AAAAGAAACCAACAGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCCCCCC--------GGGCCCGAGTTGTAATTTGCAGAGGATGCTTTCGGTG-CGGCCCCTTCTGAGTCCCCTGGAATGGGGCGCCACAGAGGGTGAGAGCCCCGTATAGTCGGACGCCAAACCGGTGTAAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTAAATTTCTTCTAAAGCTAAATATAGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACCTTGAAAAGAGGGTTAAACAGTACGTGAAATTGTTGAAAGGGAAGCGCTTGTGACCAGACT-CGCGCCCGGCGGATC-ATCCAGCG-----TTCT-CGCT-GGTGCGCTCCG-CCG-GG--CTCGGGCCAGCATCGGTTTCCGCCGGGGGACAAAGG-CGCCGGGAACGTGG-CTC--CCTTCGGGGA-GTG-GGTAGCC-CG-GCGTGCAATGCCCCGG--------CGGGGA--CCGAGGACC Ophioceras_tenuisporum_AY346295_ AAAAGAAACCAACAGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCCCCCC--------GGGCCCGAGTTGTAATTTGCAGAGGATGCTTTCGGTG-CGGCCCCTTCTGAGTCCCCTGGAATGGGGCGCCACAGAGGGTGAGAGCCCCGTATAGTCGGACGCCAAACCGGTGTAAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTAAATTTCTTCTAAAGCTAAATATAGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACCTTGAAAAGAGGGTTAAACAGTACGTGAAATTGTTGAAAGGGAAGCGCTTGTGACCAGACT-CGCGCCCGGCGGATC-ATCCAGCG-----TTCT-CGCT-GGTGCGCTCCG-CCG-GG--CTCGGGCCAGCATCGGTTTCCGCCGGGGGACAAAGG-CGCCGGGAACGTGG-CTCC-CC-TAGGGGA-GTGTTATAGCC-CG-GCGTGCAATGCCCTGG--------CGGGGA--CCGAGGACC F520 AAAAGAAACCAACAGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCCC----T------AGGCCCGAGTTGTAATTTGTAGAGGATGCTTTGGGCG-GAGTGCTTACCGAGTCCCCTGGAATGGGGCGCCACAGAGGGTGAGAGCCCCGTATGGTTTGCCACTGAACCCATGTAAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTAAATTTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGCACGTGAAATTGTTGAAAGGGAAGCGCTTGTGACCAGACT-TGCGCCCGGCGGATC-ATCCAGGG-----TTCT-CCCT-GGTGCACTCCG-CCG-GG--CTCAGGCCAGCATCGGTTTTCGCCGGGGGACAAAAG-CTTCGGGAACGGGG-C----------------------------------------------------------------------- Buergenerula_spartinae_DQ341492_ AAAAGAAACCAACAGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCCC----T------AGGCCCGAGTTGTAATTTGCAGAGGATGCTTTTGGTG-ACGCGCCTACCGAGTCCCCTGGAACGGGGCGCCACAGAGGGTGAGAGCCCCGTATGGTTTGACGCCGAGCCTCTGTAAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTAAATTTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGCACGTGAAATTGTTGAAAGGGAAGCGCTCGTGACCAGACT-TGCGCCGGGCGGATC-ATCCAGCG-----TTCT-CGCT-GGTGCACTCCG-CCC-GG--CTCAGGCCAGCATCGGTTTTCGCCGGGGGACAAAAG-CTTCGGGAACGTAG-CTC--CCTTCGGGGA-GTGTTATAGCC-CG-TTGCGCAATACCCCGG--------CGGGGA--CCGAGGACC Magnaporthe_salvinii_DQ341498_ AAAAGAAACCAACAGGGATTGCCCTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCCC----T------AGGCCCGAGTTGTAATTTGCAGAGGATGCTTTTGGTG-AAGCGCTTACCGAGTCCCCTGGAACGGGGCGCCACAGAGGGTGAGAGCCCCGTATGGTTTGACGCCGAGCCTCTGTAAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAACGGGAGGTAAATTTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGCACGTGAAATTGTTGAAAGGGAAGCGCTCGTGACCAGACT-TGCGCCGGGCGGATC-ATCCAGCG-----TTCT-CGCT-GGTGCACTCCG-CCC-GG--CTCAGGCCAGCATCGATTTTCGCCGGGGGACAAAAG-CTTCGGGAACGTGG-CTC-TC-TTCGGGGA-GTGTTATAGCC-CG-TTGCGTAATACCCCGG--------CGGGGA--TCGAGGACC Muraeriata_collapsa_EU527996_ --------------------------------------------GCAACAGCTCAAATTTGAAATCCGGCCTTTTTTAAAAAAAGGTCTGAGTTGTAATTTGCAGAGGATGCTTTTGGCGTAAGCGCTTACCAAGTCCTTTGGAATAAGGCGCCGTAGAGGGTGAGAGCCCCGTATGGTTTGACGCTGAGCCTTTATAAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAACGGGAGGTAAATTTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAAAAGCACGTGAAATTGTTGAAAGGGAAGCGCTAGTGATCAGACT-TGCTCCGGGCGGATC-ATCCGGTGGATTTTTCTCCGCT-GGTGCACTCCG-CTTCGG--TTCAGGCCAGCATCGGCTTCCCCCGGGAGACAAAAG-CTTGGGGAACGTGG-CTC-TC-TTAGGAGG-GTGTTATAGCCCTGTTTGCATAATATCCCGGGTCTTTTTTAAGGAGGCCGAGGACC Muraeriata_africana_EU527995_ -----------------------------------------GCGGCAACAGCTCAAATTTGAAATCTGGCCCCCC--------GGGCCCGAGTTGTAATTTGCAGAGGATGCTTTTGGCG-AAGCGCTTACCGAGTCCCCTGGAATGGGGCGCCACAGAGGGTGAGAGCCCCGTATGGTTCGCCGCCGAGCCTTTGTAAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAACGGGAGGTAAATTTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAAAAGCACGTGAAATTGTTGAAAGGGAAGCGCTAGTGACCAGACT-TGCGCCGGGCGGATC-ATCCGGCG---TTTTTT-CGCC-GGTGCACTCCGCCCC-GG--CTCAGGCCAGCATCGGCTTCCGCCGGGGGACAAAAG-CTCGGGGAACGTGGCCT--TC-TTCGGAGG-GTGTTATAGCCTCG-CTGCACAATGCCCCGG--------CGGGGG--CCGAGGACC Gaeumannomyces_medullaris_FJ176854_ AAAAGAAACCAACAGGGATTGCCCTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCCC----A------AGGCCCGAGTTGTAATTTGCAGAGGATGCTTTTGGTG-AGGCGCTTACCGAGTCCCCTGGAATGGGGCGCCACAGAGGGTGAGAGCCCCGTATGGTTTGCCGCCGAGCCTCTGTAAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTAAATTTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGCACGTGAAATTGTTGAAAGGGAAGCGCTCGTGACCAGACT-TGCGCCGGGCGGATCAATTCAGCC-----TTCG-GGCTGGGTGCGCTCTG-CCC-GG--CTCAGGCCAGCATCGGTTTTCGCCGGGGGATAAAAG-CTTCGGGAACGTAG-CTC--CCTACGGGGA-GTGTTATAGCC-CG-TTGCATAATACCCCGG--------CGGGGA--CCGAGGACC Gaeumannomyces_cylindrosporus_DQ341494_ AAAAGAAACCAACAGGGATTGCCCTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCCC----T------AGGCCCGAGTTGTAATTTGCAGAGGATGCTTTTGGTG-AGGTGCTTACCGAGTCCCCTGGAATGGGGCGCCACAGAGGGTGAGAGCCCCGTATGGTTTGACGCCGAGCCTCTGTAAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTAAATTTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGCACGTGAAATTGTTGAAAGGGAAGCGCTCGTGACCAGACT-TGCGCCGGGCGGATC-ATCCAGCG-----TTCT-CGCT-GGTGCACTCCG-CCC-GG--CTCAGGCCAGCATCGGTTTTCGCCGGGGGACAAAAG-CTTCGGGAACGTAG-CTCCTC--TCGGGGA-GTGTTATAGCC-CG-TTGCATAATACCCCGG--------CGGGGA--CCGAGGACC ; END; BEGIN TREES; Title MagnaporthaceaeMB; LINK Taxa = Taxa; TRANSLATE 1 Chaetomium_globosum_AY346272_, 2 Chaetomium_microascoides_AY346273_, 3 F504, 4 Ophioceras_tenuisporum_AY346295_, 5 F520, 6 Buergenerula_spartinae_DQ341492_, 7 Magnaporthe_salvinii_DQ341498_, 8 Muraeriata_collapsa_EU527996_, 9 Muraeriata_africana_EU527995_, 10 Gaeumannomyces_medullaris_FJ176854_, 11 Gaeumannomyces_cylindrosporus_DQ341494_; TREE con_50_majrule = (1:0.012176,2:0.020657,((3:0.00779,4:0.005182)1.00:0.067546,(((5:0.054609,(8:0.091533,9:0.024378)1.00:0.032391)0.51:0.009596,7:0.01042,10:0.024484,11:0.003841)0.55:0.007162,6:0.008918)0.99:0.038771)1.00:0.066156); TREE con_50_majrule = (1:0.012176,2:0.020657,((3:0.00779,4:0.005182):0.067546,(((5:0.054609,(8:0.091533,9:0.024378):0.032391):0.009596,7:0.01042,10:0.024484,11:0.003841):0.007162,6:0.008918):0.038771):0.066156); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 569; 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 - 569; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 569; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1374683910596; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 4445451051784126773; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 1728598821266858742; mqVersion 275; checksumv 0 3 3774480477 null getNumChars 569 numChars 569 getNumTaxa 11 numTaxa 11 short true bits 15 states 15 sumSquaresStatesOnly 108980.0 sumSquares 108980.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 179; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 700 464; setLocation 120 47; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #4445451051784126773 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #4445451051784126773; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 521 397; setLocation 120 47; 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 #4445451051784126773 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 865.1307783876096.3787515089863143680; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 521 397; setLocation 120 47; 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 '(2:0.0103285,(1:0.012176,((3:0.00779,4:0.005182)1.00:0.067546,(6:0.008918,(7:0.01042,10:0.024484,11:0.003841,(5:0.054609,(8:0.091533,9:0.024378)1.00:0.032391)0.51:0.009596)0.55:0.007162)0.99:0.038771)1.00:0.066156):0.0103285);'; 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 #1728598821266858742 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 521 397; setLocation 120 47; 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;