#NEXUS [written Wed Jul 24 16:59:07 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=12; TAXLABELS Starmera_caribaea_EF550284_ Starmera_amethionina_Var_pachycereana_EF550283_ Pichia_maclurae_EF550310_ Pichia_jadinii_EF550309_ Pichia_petersonii_EF550311_ Pichia_misumaiensis_EF550306_ Pichia_lachancei_EF550313_ Williopsis_saturnus_Var_saturnus_EU541541_ Williopsis_saturnus_Var_suaveolens_EU544674_ Williopsis_saturnus_Var_mrakii_U94929_ F271_LSU Williopsis_saturnus_Var_subsufficiens_U75960_ ; END; BEGIN CHARACTERS; TITLE WilliopsisMB; DIMENSIONS NCHAR=554; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Starmera_caribaea_EF550284_ AAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTGGTA--GTT-TCACTGCCCGAGTTGTAATTTGAAGAACG-GTTCTTGTAGCGCAGCC-TTTGTCTATGTTCCTTGGAACAGGACGTCACAGAGGGTGAGAATCCCGTGAGATGGGGGG--TGT-GCT-GC---TTGTAGAGCCAGTTCGACGAGTCGAGTTGTTTGGGAATGCAGCTCTAAGTGGGTGGTAAATTCCATCTAAAGCTAAATATTGGCGAGAGACCGATAGCGAACAAGTACAGTGATGGAAAGATGAAAAGAACTTTGAAAAGAGAGTGAAAAAGTACGTGAAATTGTTGAAAGGGAAGGGCATTTGATCAGACTTGGTGGGGGA--GTA-CTGGCAGGCACTTGTTG-CCTGTTTACT-GCT-C-TCTTGCTGGGCCAGCATCGATTCGTGTGGCAGGACAACCGGCTG--GGAACGTGG--CTGCT----T---GCAGTG---TTATAGCCCAGCCTTCTACTGCCTACGTGGATCGAGG Starmera_amethionina_Var_pachycereana_EF550283_ AAACCAACAGGGATTGCCTTAGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTGGTA--GTT-TCACTGCCCGAGTTGTAATTTGAAGAACG-GTTCTTGTAGCGCGGCC-TTTGTCTATGTTCCTTGGAACAGGACGTCACAGAGGGTGAGAATCCCGTGAGATGGGGGC--AGC-GCT-GC---TTGTAGGGCCAGTTCGACGAGTCGAGTTGTTTGGGAATGCAGCTCTAAGTGGGTGGTAAATTCCATCTAAAGCTAAATATTGGCGAGAGACCGATAGCGAACAAGTACAGTGATGGAAAGATGAAAAGAACTTTGAAAAGAGAGTGAAAAAGTACGTGAAATTGTTGAAAGGGAAGGGCATTTGATCAGACTTGGTGGGGGA--GTA-CTGGCGTCCACTTGTTGGGC-GTTTACT-GCTGC-TCT-GCTGGGCCAGCATCGATTCGTGTGGCAGGACAACCGGCTG--GGAACGTGG--CTGCATTTTT---GCAGTG---TTATAGCCCATCCTTCTGCTGCCTACATGGATCGAGG Pichia_maclurae_EF550310_ AAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTGGT---GTTTTTACA-CCCGAGTTGTAATTTGAAGAAGGATTTCTGGCA-CA-GGCCCCCCGTCTATGTTCCTTGGAACAGGACGTCACAGAGGGTGAGAATCCCGTCTGGCGGGGAGGGACC-AGTGGCA--TTGTAGATTTCCTTCGACGAGTCGAGTTGTTTGGGAATGCAGCTCTAAGTGGGTGGTAAATTCCATCTAAAGCTAAATATTGGCGAGAGACCGATAGCGAACAAGTACAGTGATGGAAAGATGAAAAGAACTTTGAAAAGAGAGTGAAAAAGTACGTGAAATTGTTGAAAGGGAAGGATATTGGATCAGACTTGGTGTTGGACGGTACCT--CG-CCACTTGTTGGCGGGATCACCCG-TTCCTC--ACTGGGCCAGCATCGGTTTTTGCGGCGGGATAATTG-CTCAGGGAACGTGGCTCTGCC-TTTT-AGGCCGAGTGTTTATAGCCCTGGCACATACCGCCTGCGTGGACCGAGG Pichia_jadinii_EF550309_ AAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTG--AGGCTC-TCAGCCCCCGAGTTGTAATTTGAAGATGGTGTTCTGGT-GCC-GGCCCCCTGTCTACGTTCCTTGGAACAGGACATCACAGAGGGTGAGAATCCCGTCTGGCGGGGCG--GCC---TGGCTCCGTGTAGAGCGCCATCGACGAGTCGAGTTGTTTGGGAATGCAGCTCTAAGTGGGTGGTAAATTCCATCTAAAGCTAAATATTGGCGAGAGACCGATAGCGAACAAGTACAGTGATGGAAAGATGAAAAGAACTTTGAAAAGAGAGTGAAAAAGTACGTGAAATTGTTGAAAGGGAAGGGTATTGGATCAGACTTGGTGCTGTG-CGAA--TAGCGG-CTCTTCTTGGGCTGCCCACTCGCA-C-TCC-ACCGGGCCAGCATCGGTTTGGGCGGCAAGACAAT-GGCGGG-GGAACGTGGCACTGCT---CTCGGGCAGTGTGTTTATAGCCCCCGCTGATGTTGCCTGCCTAGACCGAGG Pichia_petersonii_EF550311_ AAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAAGAGCTCAAATTTGAAATCCGGTA--CTT-TCAGTGCCCGAGTTGTAATTTGAAGATAGTTTTCTGGC-GCC-GGCC-CTTGTCTATGTTCCTTGGAACAGGACGTCATGGAGGGTGAGAATCCCGTGTGGCGGGGAG--CCC-GGT-GCT--GTGTAGATTTCTATCGACGAGTCGAGTTGTTTGGGAATGCAGCTCTAAGTGGGTGGTAAATTCCATCTAAAGCTAAATACTGGCGAGAGACCGATAGCGAACAAGTACAGTGATGGAAAGATGAAAAGAACTTTGAAAAGAGAGTGAAAAAGTACGTGAAATTGTTGAAAGGGAAGGGTATTGGATCAGACTTGGTGTTGTG-CGAT--TATCTT-CTCCTCGTGGGTTGTGCACTCG-TGCCTC--ACTGGGCCAGCATCGGTTTGGGCGGCAGGACAAT-GGCGGG-GGAATGTGGCACTTTA---------C-GTGTG-TTATAGCCCTTGCTGATACTGCCTGCCTGGACCGAGG Pichia_misumaiensis_EF550306_ AAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTGGTA-CCTC-T-GGTGCCCGAGTTGTAATTTGAAGATAGTTTTCTGGTATTG-GGCC-CTTGTCTATGTTCCTTGGAACAGGACGTCATAGAGGGTGAGAATCCCGTCTGGCGGGGCG--CCC-TTT-GCT--ATGTAGATTTCTATCGACGAGTCGAGTTGTTTGGGAATGCAGCTCTAAGTGGGTGGTAAATTCCATCTAAAGCTAAATATTGGCGAGAGACCGATAGCGAACAAGTACAGTGATGGAAAGATGAAAAGAACTTTGAAAAGAGAGTGAAAAAGTACGTGAAATTGTTGAAAGGGAAGGATATTGGATCAGACTTGGTGTTGCA-TGAT--TATCTT-CCCCTTGTGGGTTGTGCACTCG-TGCTTC--ACTGGGCCAGCATCGGTTCGGACGGCAAGATAAT-GACATTGGGAACGTGGCTCTTTC---TTCGGTTAGAGTG-TTATAGCCCATGTTGATGTTGCCTGCCTGGACCGAGG Pichia_lachancei_EF550313_ AAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTGGTA-CCT--GCGGTGCCCGAGTTGTAATTTGAAGATAGTTTTCTGGTTTC--GGCC-CCTGTCTATGTTCCTTGGAACAGGACGTCACAGAGGGTGAGAATCCCGTCTGGCGGGGTG--TCCGATT-CC---GTGTAGATTTCTATCGACGAGTCGAGTTGTTTGGGAATGCAGCTCTAAGTGGGTGGTAAATTCCATCTAAAGCTAAATATTGGCGAGAGACCGATAGCGAACAAGTACAGTGATGGAAAGATGAAAAGAACTTTGAAAAGAGAGTGAAAAAGTACGTGAAATTGTTGAAAGGGAAGGGTATTAGATCAGACTTGGTGTTTAG-TGAT--TATCTT-CCCCTCGTGGGTTGTGCACTCGCT-CTTC--ACTGGGCCAGCATCGGTTCGGGTGGCAGGATAAT-GGCATG-GGAACGTGGCACCGTC---TTCGGGCGGTGTG-TTATATCCCACGCTGATGCTGCCTGCCTGGACCGAGG Williopsis_saturnus_Var_saturnus_EU541541_ AAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTGGTA-CCTT-T-GGTGCCCGAGTTGTAATTTGAAGATAGTTTTCTGGT-GCT-GGCC-CTTGTCTATGTTCCTTGGAACAGGACGTCACAGAGGGTGAGAATCCCGTCTGGCGGGGTG--TCC-AGT-GCT--TTGTAGATTTCTATCGACGAGTCGAGTTGTTTGGGAATGCAGCTCTAAGTGGGTGGTAAATTCCATCTAAAGCTAAATATTGGCGAGAGACCGATAGCGAACAAGTACAGTGATGGAAAGATGAAAAGAACTTTGAAAAGAGAGTGAAAAAGTACGTGAAATTGTTGAAAGGGAAGGGTATTAGATCAGACTTGGTGTTTTG-TGAT--TATCTT-CCCTTCTTGGGTTGTGCACTCGCA-TTTC--ACTGGGCCAGCATCGGTTCGGGTGGTAAGATAAT-GACATT-GGAACGTGGCACTGCC---TTCGGGTGGTGTG-TTATAGCCCTTGTTGATGTTGCCTATCTGGACCGAGG Williopsis_saturnus_Var_suaveolens_EU544674_ AAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTGGTA-CCTT-T-GGTGCCCGAGTTGTAATTTGAAGATAGTTTTCTGGT-GCT-GGCC-CTTGTCTATGTTCCTTGGAACAGGACGTCACAGAGGGTGAGAATCCCGTCTGGCGGGGTG--TCC-AGT-GCT--TTGTAGATTTCTATCGACGAGTCGAGTTGTTTGGGAATGCAGCTCTAAGTGGGTGGTAAATTCCATCTAAAGCTAAATATTGGCGAGAGACCGATAGCGAACAAGTACAGTGATGGAAAGATGAAAAGAACTTTGAAAAGAGAGTGAAAAAGTACGTGAAATTGTTGAAAGGGAAGGGTATTAGATCAGACTTGGTGTTTTG-TGAT--TATCTT-CCCTTCTTGGGTTGTGCACTCGCA-TTTC--ACTGGGCCAGCATCGGTTCGGGTGGTAAGATAAT-GACATT-GGAACGTGGCACTGCC---TTCGGGTGGTGTG-TTATAGCCCTTGTTGATGTTGCCTACCTGGACCGAGG Williopsis_saturnus_Var_mrakii_U94929_ AAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTGGTA-CCT--TCGGTGCCCGAGTTGTAATTTGAAGATAGTTTTCTGGT-GCT-GGCC-CTTGTCTATGTTCCTTGGAACAGGACGTCACAGAGGGTGAGAATCCCGTCTGGCGGGGTG--TCC-AGT-GCT--TTGTAGATTTCTATCGACGAGTCGAGTTGTTTGGGAATGCAGCTCTAAGTGGGTGGTAAATTCCATCTAAAGCTAAATATTGGCGAGAGACCGATAGCGAACAAGTACAGTGATGGAAAGATGAAAAGAACTTTGAAAAGAGAGTGAAAAAGTACGTGAAATTGTTGAAAGGGAAGGGTATTAGATCAGACTTGGTGTTTTG-TGAT--TATCTT-CCCTTCTTGGGTTGTGCACTCGCA-TTTC--ACTGGGCCAGCATCGGTTCGGGTGGTAAGATAAT-GACATT-GGAACGTGGCACTGCC---TTCGGGTGGTGTG-TTATAGCCCTTGTTGATGTTGCCTACCTGGACCGAGG F271_LSU AAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTGGTA-CCT--TCGGTGCTCGAGTTGTAATTTGAAGATAGTTTTCTGGT-GCT-GGCC-CTTGTCTATGTTCCTTGGAACAGGACGTCACAGAGGGTGAGAATCCCGTCTGGCGGGGTG--TCC-AGT-GCT--TTGTAGATTTCTATCGACGAGTCGAGTTGTTTGGGAATGCAGCTCTAAGTGGGTGGTAAATTCCATCTAAAGCTAAATATTGGCGAGAGACCGATAGCGAACAAGTACAGTGATGGAAAGATGAAAAGAACTTTGAAAAGAGAGTGAAAAAGTACGTGAAATTGTTGAAAGGGAAGGGTATTAGATCAGACTTGGTGTTTTG-TGAT--TATCTT-CCCTTCTTGGGTTGTGCACTCGCA-TTTC--ACTGGGCCAGCATCGGTTCGGATGGCAAGATAAT-GACATT-GGAACGTGGCACTACC---TTCGGGTGGTGTA-TTATAGCCCTTGTTGATGTTGCCTATCTGGACCGAGG Williopsis_saturnus_Var_subsufficiens_U75960_ AAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTGGTA-CCT--TCGGTGCCCGAGTTGTAATTTGAAGATAGTTTTCTGGT-GCT-GGCC-CTTGTCTATGTTCCTTGGAACAGGACGTCACAGAGGGTGAGAATCCCGTCTGGCGGGGTG--TCC-AGT-GCT--TTGTAGATTTCTATCGACGAGTCGAGTTGTTTGGGAATGCAGCTCTAAGTGGGTGGTAAATTCCATCTAAAGCTAAATATTGGCGAGAGACCGATAGCGAACAAGTACAGTGATGGAAAGATGAAAAGAACTTTGAAAAGAGAGTGAAAAAGTACGTGAAATTGTTGAAAGGGAAGGGTATTAGATCAGACTTGGTGTTTTG-TGAT--TATCTT-CCCTTCTTGGGTTGTGCACTCGCA-TTTC--ACTGGGCCAGCATCGGTTCGGATGGCAAGATAAT-GACATT-GGAACGTGGCACTACC---TTCGGGTGGTGTG-TTATAGCCCTTGTTGATGTTGCCTATCTGGACCGAGG ; END; BEGIN TREES; Title WilliopsisMB; LINK Taxa = Taxa; TRANSLATE 1 Starmera_caribaea_EF550284_, 2 Starmera_amethionina_Var_pachycereana_EF550283_, 3 Pichia_maclurae_EF550310_, 4 Pichia_jadinii_EF550309_, 5 Pichia_petersonii_EF550311_, 6 Pichia_misumaiensis_EF550306_, 7 Pichia_lachancei_EF550313_, 8 Williopsis_saturnus_Var_saturnus_EU541541_, 9 Williopsis_saturnus_Var_suaveolens_EU544674_, 10 Williopsis_saturnus_Var_mrakii_U94929_, 11 F271_LSU, 12 Williopsis_saturnus_Var_subsufficiens_U75960_; TREE con_50_majrule = (1:0.016062,2:0.020567,(3:0.080211,(4:0.060488,(5:0.03783,((6:0.051288,((8:0.002309,(11:0.005914,12:0.001985)0.98:0.007619)0.68:0.00384,9:0.001958,10:0.001984)1.00:0.026062)0.76:0.016621,7:0.026476)1.00:0.034686)0.98:0.032742)1.00:0.077948)1.00:0.117207); TREE con_50_majrule = (1:0.016062,2:0.020567,(3:0.080211,(4:0.060488,(5:0.03783,((6:0.051288,((8:0.002309,(11:0.005914,12:0.001985):0.007619):0.00384,9:0.001958,10:0.001984):0.026062):0.016621,7:0.026476):0.034686):0.032742):0.077948):0.117207); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 554; 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 - 554; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 554; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1374685147129; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 1146075291277681135; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 6928562290100581795; mqVersion 275; checksumv 0 3 3379979623 null getNumChars 554 numChars 554 getNumTaxa 12 numTaxa 12 short true bits 15 states 15 sumSquaresStatesOnly 142625.0 sumSquares 142625.0 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 1161 712; setLocation 52 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #1146075291277681135 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #1146075291277681135; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1044 645; setLocation 52 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 #1146075291277681135 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 865.1305408092028.9096057101185303634; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1044 645; setLocation 52 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 '(1:0.008031,(2:0.020567,(3:0.080211,(4:0.060488,(5:0.03783,(7:0.026476,(6:0.051288,(9:0.001958,10:0.001984,(8:0.002309,(11:0.005914,12:0.001985):0.007619):0.00384):0.026062):0.016621):0.034686):0.032742):0.077948):0.117207):0.008031);'; 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 #6928562290100581795 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1044 645; setLocation 52 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;