#NEXUS [written Sat Jul 02 22:52:08 EEST 2011 by Mesquite version 2.74 (build 550) at antrodiella/128.214.62.108] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=7; TAXLABELS Cyanotrama_gypsea_CN Cyanotrama_gypsea_CN_3 Cyanotrama_gypsea_CN_2 Cyanotrama_rimosa_IR Cyanotrama_thujae_CN Cyanotrama_rimosa_US_2 Cyanotrama_rimosa_US ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=575; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Cyanotrama_gypsea_CN AGGATCATTATCGAGTTTGAAAGTGGGCTTTGATGCTGGCGTCTCTCCAGGCGCATGTGCTCAGCCCCGCTCATCCACTCAACCCCTGTGCACTTCGTCGGAGTCAATGGGTCG-CTCTTGCGGCTTTTGGCTTTGACTTATCATTTACAAACGC-TTTACTTGTCTTGTAGAATGTAATGCCTCTTGTTGGGCGAAATTAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGCATTCCGAGGAGCATGCCTGTTTGAGTGTCATGTTAATCTCAATCCCTTGGGTTTGTTATGAACTCTTGAGATTGGACTTGGAGGTTACTGCTGGCTTCACCGTCGGCTCCTCTTGAATGTATTAGCTGGGCCTTTAGCCTCGCGCTCGTGGTGTGATAGTTTATTCACCTTGAGTGTGGCTTGTATGGGTCTGCTTCTAATCGTCTTAAAACGACAA-TACCTTGACTCTCTGACCTCAAATCAG Cyanotrama_gypsea_CN_3 AGGATCATTATCGAGTTTGAAAGTGGGCTTTGATGCTGGCGTCTCTCCAGGCGCATGTGCTCAGCCCCGCTCATCCACTCAACCCCTGTGCACTTCGTCGGAGTCAATGGGTCG-CTCTTGCGGCTTTTGGCTTTGACTTATCATTTACAAACGCTTTTACTTGTYTTGTAGAATGTAATGCCTCTTGTTGGGCGAAATTAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGCATTCCGAGGAGCATGCCTGTTTGAGTGTCATGTTAATCTCAATCCCTTGGGTTTGTTATGAACTCTTGAGATTGGACTTGGAGGTTACTGCTGGCTTCACCGTCGGCTCCTCTTGAATGTATTAGCTGGGCCTTTAGCCTCGCGCTCGTGGTGTGATAGTTTATTCACCTTGAGTGTGGCTTGTATGGGTCTGCTTCTAATCGTCTTAAAACGACAA-TACCTTGACTCTCTGACCTCAAATCAG Cyanotrama_gypsea_CN_2 AGGATCATTATCGAGTTTGAAAGTGGGC-TTGATGCTGGCGTCTCTCCAGGCGCATGTGCTCAGCCCCGCTCATCCACTCAACCCCTGTGCACTTCGTCGGAGTCAATGGGTCG-CTCTTGCGGCTTTTGGCTTTGACTTATCATTTACAAACGCTTTTACTTGTCTTGTAGAATGTAATGCCTCTTGTTGGGCGAAATTAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGCATTCCGAGGAGCATGCCTGTTTGAGTGTCATGTTAATCTCAATCCCTTGGGTTTGTTATGAACTCTTGAGATTGGACTTGGAGGTTACTGCTGGCTTCACCGTCGGCTCCTCTTGAATGTATTAGCTGGGCCTTTAGCCTCGCGCTCGTGGTGTGATAGTTTATTCACCTTGAGTGTGGCTTGTATGGGTCTGCTTCTAATCGTCTTAAAACGACAA-TACCTTGACTCTCTGACCTCAAATCAG Cyanotrama_rimosa_IR AGGATCATTATCGAGTTTGAAAGTGGGC-TTGATGCTGGCGTCTCTCCAGACGCATGTGCTCAGCCCCGCTCATCCACTCAACCCCTGTGCACTTCGTCGGAGTCAATGGGCCG-CTTTTGCGGCTTTTGGCTTTGACTTATCATTTACAAACGC-TTTACTTGTCATGTAGAATGTAATGCCTCTTGTTGGGCGAAATTAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGCATTCCGAGGAGCATGCCTGTTTGAGTGTCATGTTAATCTCAATCCCCTGGGTTTGTTATGAACTCTTGAGATTGGACTTGGAGG-TACTGCTGGCTTCACCGTCGGCTCCTCTTGAATGTATTAGCTGGGCCTTTAGCCTCGCGCTCGTGGTGTGATAGTTTATTCACCTTGAGTGTGGCTTGTAT-GGTCTGCTTCTAATCGTCTTAACAAGACAAATACCTTGACTCTCTGACCTCAAATCAG Cyanotrama_thujae_CN ---------------------AGTGGGC-TTGATGCTGGCGTCTCTCCAGACGCATGTGCTCAGCCCCGCTCATCCACTCAACCCCTGTGCACTTCGTCGGAGTCAATGGGCCG-CTTTTGGGGCTTTTGGCTTTGACTTATCCWTTATAAACGC-TTTACTTGTCATGTAGAATGTAATGCCTCTTGTTGGGCGAAATTAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGCATTCCGAGGAGCATGCCTGTTTGAGTGTCATGTTAATCTCARTCCCYTGGGTTTGTTATGAACTCTTGAGATTGGACTTGGAGG-TACTGCTGGCTTCACCGTCGGCTCCTCTTGAATGTATTAGCTGGGCCTTTAGCCTCGCGCTCGTGGTGTGATAGTTTATTCACCTTGAGTGTGGCTTGTAT-GGTCTGCTTCTAATCGTCTTAAC-AGACAA-TACCTTGACTCTCTGACCTCAAATCAG Cyanotrama_rimosa_US_2 AGGATCATTATCGAGTTTG-AAGTGGGC-TTGATGCTGGCGTCTCTCCAGACGCATGTGCTCAGCCCCGCTCATCCACTCAACCCCTGTGCACTTCGTCGGAGTCAATGGGTCGA--TTTGCGGCCTTTGGCTTTGACTTATCA-TTATAAACGC-TTTACTTGTTATGTAGAATGTAATGCCTCTTGTTGGGCGAAATTAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGCATTCCGAGGAGCATGCCTGTTTGAGTGTCATGTTAATCTCAATCCCCTGGGTTTGTTATGAACTCTTGAGATTGGACTTGGAGG-TACTGCTGGCTTCACCGTCGGCTCCTCTTGAATGTATTAGCTGGGCCTTTAGCCTCGCGCTCGTGGTGTGATAGTTTATTCACCTTGAGTGTGGCTTGTAT-GGTCTGCTTCTAATCGTCTTAAT-AGACAA-TACCTTGACTCTCTGACCTCAAATCAG Cyanotrama_rimosa_US -----CATTATCGAGTTTG-AAGTGGGC-TTGATGCTGGCGTCTCTCCAGACGCATGTGCTCAGCCCCGCTCATCCACTCAACCCCTGTGCACTTCGTCGGAGTCAATGGGTCGA--TTTGCGGCCTTTGGCTTTGACTTATCA-TTATAAACGC-TTTACTTGTTATGTAGAATGTAATGCCTCTTGTTGGGCGAAATTAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGCATTCCGAGGAGCATGCCTGTTTGAGTGTCATGTTAATCTCAATCCCCTGGGTTTGTTATGAACTCTTGAGATTGGACTTGGAGG-TACTGCTGGCTTCACCGTCGGCTCCTCTTGAATGTATTAGCTGGGCCTTTAGCCTCGCGCTCGTGGTGTGATAGTTTATTCACCTTGAGTGTGGCTTGTAT-GGTCTGCTTCTAATCGTCTTAAT-AGACAA-TACCTTGACTCTCTGACCTCAAATCAG ; END; BEGIN MRBAYES; Lset applyto = ( all ) nst = 1 rates = propinv; mcmcp ngen = 8000000 printfreq = 4000 samplefreq = 4000 diagnfreq = 100000 nchains = 8 nruns = 3 temp = 0.08; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 575; END; BEGIN TREES; Title 'Trees from "Cyan_ssF81i.nex.con"'; LINK Taxa = Taxa; TRANSLATE 1 Cyanotrama_gypsea_CN, 2 Cyanotrama_gypsea_CN_3, 3 Cyanotrama_gypsea_CN_2, 4 Cyanotrama_rimosa_IR, 5 Cyanotrama_thujae_CN, 6 Cyanotrama_rimosa_US_2, 7 Cyanotrama_rimosa_US; TREE con_50_majrule = (1:0.00294,2:0.003158,3:0.0030,((4:0.008856,5:0.015908)0.57:0.030978,(6:0.003118,7:0.003127)0.94:0.031332)0.99:0.075632); TREE con_50_majrule = (1:0.00294,2:0.003158,3:0.0030,((4:0.008856,5:0.015908):0.030978,(6:0.003118,7:0.003127):0.031332):0.075632); END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 575; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 575; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1309636328515; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 1584607080345020349; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 449589263884759716; mqVersion 274; checksumv 0 2 2594684453 null getNumChars 575 numChars 575 getNumTaxa 7 numTaxa 7 short true bits 2305843009213693967 states 15 sumSquaresStatesOnly 100267.0 sumSquares -9.2233720368547512E18 NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 479; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 899 464; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #1584607080345020349 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #1584607080345020349; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 420 397; setLocation 8 8; 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.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #1584607080345020349 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1076.1309636082953.829758058803946058; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 420 397; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; showPage 4; setActive; 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 6; orientUp; 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; 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 #449589263884759716 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 420 397; setLocation 8 8; 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.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;