#NEXUS [written Tue Jun 12 14:07:17 CST 2012 by Mesquite version 2.75 (build 564) at YuIto-PC/10.226.147.91] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=7; TAXLABELS Ruppia_cirrhosa_B Ruppia_maritima_B Ruppia_maritima_D Ruppia_maritima_F Ruppia_maritima_E 'Ruppia maritima B''''''' 'Ruppia maritima E''' ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=712; FORMAT DATATYPE = DNA INTERLEAVE GAP = - MISSING = N; MATRIX Ruppia_cirrhosa_B TTTCCGTAGGTGAACCTGCGGAAGGATCATTGTCGAGATGGATAGCAATAGACGAACACGTCACCGAATTATTTTGGAAAAGTGCGTTTTTGATGCA-TTTGTCCTAGCAGAAATGCTATGCTCCCTTTGGGCGTGTGTGCATTTGTGCTCAACAACCAACCCTGGCACAACTTGTGTCAAGCAAAAAGTAGCTTGTGGTTTGTCTCCTTCATCGTATTGAGA-GGATCGCGAGTCTCACAGAATTACTATTAAATGCATGACTCCCGTCAACGGATATCTTGGCCCTTGCATCGATGAAGAACGTAGCAAAATGCGATACTTGATGTGAATTGTAGAATCCCGTGAACCATCGAGTCTTTGAATGCAAGTTGCGCCCGAAGTTGTTAGACGGACGGCATGCCTGCCTGGGCGTCATTAATTGAGTCGCTCATTAAGTATGATCTTCATGGTTGATGAAGCGGATTATGGCCTTCTGGGAATTATCCGGTAGGCTTAAATGGGCGTGACCTGCTGTGTGGAGATGCACGATGGGTGGTGAACTTTTGTGGATTGTAGTCGATCCCATCATTAGCGAATAGCACGTCGTGCCTCCCTCAACATCTTCTTTCACGTGCTTACCCTTTGCATAAGGTGTCTCGTTGGTGCCTTAATTGAACAGTAGAGAATCTGATTGGGACCTCAGGTCAGGCAAGACCACCTGCTGAGTTTAA Ruppia_maritima_B -TSTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTCGAGATGGATAGTAATAAACGAACACGTCACCGAATTATTTTGGAAGGGTGTGTTTTTGATGCACTTTATCCTAGCGGAAATGTTATGCTCCCTTTGGG--TGTGTGCATTTGTGCTTAACAACCAACCCTGGCACAACTTGTGTCAAGCAAAATGTAGCTTGTGGTTTGTCTCCTTCATTGTATTGAGATAGATCGTGAGTCTCCCAGAATTACCATTAAATGCATGACTCCCGTCAACGGATATCTTGGCCCTTGCATCGATGAAGAACGTAGCAAAATGCGATACTTGATGTGAATTGTAGAATCCCGTGAACCATCGAGTCTTTGAATGCAAGTTGCGCCCGAAGTTGTTAGACGGACGGCATGCCTGCCTGGGCGTCATTAAATGAGTCGCTCATTAAGTATGATCTTCATGGTTGATGAAGCGGATTTTGGCCTTCTGGGAGTTTTCCAGTAGGCTTAAATGGGCGTGACCTGCTGTGTGGAGATGCACGATGGGTGGTGAACATTTGTGAATTGCAGTTGATCCCATCATTAGCAAATAGCACGTCGTGCCTCCCGCAACACCTTCTTTCACGTGCTTACCCTTTGCATAAGGCATCTTGAGGATGCTTTGATTGAACAGTAGAGAATCTGACTGGGACCTCAGGTCAGGCAAGACCACCTGCTGAGTT Ruppia_maritima_D -TATAGTAATAAACGAACACGTCACCGAATTATTTTGGAAGAGTGTGTCTTTGATGCACTTTATCCTAGCGGAAATGTTACGCTCCCTTCGGG--TGTGTGCATTTGTGCTTAACAACCAACCCTGGCACAACTTGTGTCAAGCAAAATGTAGCTTGTGGTTTGTCTCCTTCATTGTATTGAGATAGATCGTGAGTCTCACAGAATTACCATTAAATGCATGACTCCCGTCAACGGATATCTTGGCCCTTGCATCGATGAAGAACGTAGCAAAATGCGATACTTGATGTGAATTGTAGAATCCCGTGAACCATCGAGTCTTTGAATGCAAGTTGCGCCCGAAGTTGTTAGACGGACGGCATGCCTGCCTGGGCGTCATTAAATGAGTCGCTCATTAAGTATGATCTTCATGGTTGATGAAGCGGATTTTGGCCTTCTGGGAGTTTTCCAGTAGGCTTAAATGGGCGTGACCTGCTGTGTGGAGATGCACGATGGGTGGTGAACATTTGTGAATTGCAGTTGATCCCATCATTAGCAAATAGCACGTCGTGCCTCCCTCAACACCTTCTTTCACGTGCTTACCCTTTGCATAAGGCATCTTGTGGATGCTTTGATTGAACAGTAGAGAATCTGATTGGGACCTCAGGTCAGGCAAGACCACCTGCTGAGTTTAA--------------------------------------- Ruppia_maritima_F -TSTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTCGAGATGGATAGTAATAAACGAACACGTCACCGAATTATTTTGGAAGAGTGTGTCTTTGATGCACTTTATCCTAGCGGAAATGTTACGCTCCCTTCGGG--TGTGTGCATTTGTGCTTAACAACCAACCCTGGCACAACTTGTGTCAAGCAAAATGTAGCTTGTGGTTTGTCTCCTTCATTGTATTGAGATAGATCGTGAGTCTCACAGAATTACCATTAAATGCATGACTCCCGTCAACGGATATCTTGGCCCTTGCATCGATGAAGAACGTAGCAAAATGCGATACTTGATGTGAATTGTAGAATCCCGTGAACCATCGAGTCTTTGAATGCAAGTTGCGCCCGAAGTTGTTAGACGGACGGCATGCCTGCCTGGGCGTCATTAAATGAGTCGCTCATTAAGTATGATCTTCATGGTTGATGAAGCGGATTTTGGCCTTCTGGGAGTTTTCCAGTAGGCTTAAATGGGCGTGACCTGCTGTGTGGAGATGCACGATGGGTGGTGAACATTTGTGAATTGCAGTTGATCCCATCATTAGCAAATAGCACGTCGTGCCTCCCTCAACACCTTCTTTCACGTGCTTACCCTTTGCATAAGGCATCTTGTGGATGCTTTGATTGAACAGTAGAGAATCTGATTGGGACCTCAGGTCAGGCAAGACCACCTGCTGAGTT Ruppia_maritima_E --TGTGTGCATTTGTGCTTAACAACCAACCCTGGCACAACTTGTGTCAAGCAAAATGTAGCTTGTGGTTTGTCTCCTTCATTGTATTGAGATAGATCGTGAGTCTCACAGAATTACCATTAAATGCATGACTCCCGTCAACGGATATCTTGGCCCTTGCATCGATGAAGAACGTAGCAAAATGCGATACTTGATGTGAATTGTAGAATCCCGTGAACCATCGAGTCTTTGAATGCAAGTTGCGCCCGAAGTTGTTAGACGGACGGCATGCCTGCCTGGGCGTCATTAAATGAGTCGCTCATTAAGTATGATCTTCATGGTTGATGAAGCGGATTTTGGCCTTCTGGGAGTTTTCCGGTAGGCTTAAATGGGCGTGACCTGCTGTGTGGAGATGCACGATGGGTGGTGAACATTTGTGAATTGCAGTTGATCCCATCATTAGCAAATAGCACGTCGTGCCTCCCTCAACGCCTTCTTTCACGTGCTTACCCTTTGCATAAGGCATCTTGTGGATGCTTTGATTGAACAGTAGAGAATCTGATTGGGACCTCAGGTCAGGCAAGACCACCTGCTGAGTTTAA------------------------------------------------------------------------------------------------------------------------------------ 'Ruppia maritima B''''''' -TSTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTCGAGATGGATAGCAATAGACGAACACGTCACCGAATTATTTTGGAAAAGTGTGTTTTTGATACACTATGTCCTAGCAGAAATGCTATGCTCCCTTTGGGCGTGTGTGCATTTGTGCTCAACAACCAACCCTGGCACAACTTGTGTCAAGCAAAAAGTAGCTTGTGGTTTGTCTCCTTCATCGTATTGAGA-GGATCGCGAGTCTCACAGAATTACTATTAAATGCACGACTCCCGTCAACGGATATCTTGGCCCTTGCATCGATGAAGAACGTAGCAAAATGCGATACTTGATGTGAATTGTAGAATCCCGTGAACCATCGAGTCTTTGAATGCAAGTTGCGCCCGAAGTTGTTAGACGGACGGCATGCCTGCCTGGGCGTCATTAATTGAGTCGCTCATTAAGTATGATCTTCATGGTTGATGAAGCGGATTATGGCCTTCTGGGAATTATCCGGTAGGCTTAAATGGGCGTGACCTGCTGTGTGGAGATGCACGATGGGTGGTGAACTTTTGTGGATTGTAGTCGATCCCATCATTAGCGAATAGCACGTCGTGCCTCCCTCAACATCTTCTTTCACGTGCTTACCCTTTGCATAAGGTGTCTCGTTGGTGCCTTAATTGAAAAGTAGAGAATCTGATTGGGACCTCAGGTCAGGCAAGACCACCTGCTGAGTT 'Ruppia maritima E''' ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 712; END; BEGIN TREES; Title 'Trees from "Ruppia_ITS.......tre"'; LINK Taxa = Taxa; TRANSLATE 1 Ruppia_cirrhosa_B, 2 Ruppia_maritima_B, 3 Ruppia_maritima_D, 4 Ruppia_maritima_F, 5 Ruppia_maritima_E, 6 'Ruppia maritima B''''''', 7 'Ruppia maritima E'''; TREE PAUP_1 = ((1:2.0,(4:3.0,7:2.0):1.0):32.0,(2:5.0,(3:0.0,5:2.0,6:2.0):3.0):0.0); TREE PAUP_2 = ((1:2.0,(4:3.0,7:2.0):1.0):31.0,(2:6.0,((3:0.0,5:2.0):1.0,6:1.0):3.0):0.0); END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 712; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 712; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1339531637958; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 252504182988083449; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 1019131953878553712; mqVersion 275; checksumv 0 3 3282268637 null getNumChars 712 numChars 712 getNumTaxa 7 numTaxa 7 short true bits 2305843009213693967 states 15 sumSquaresStatesOnly 97977.0 sumSquares -2.7670116110564327E19 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1 errorReportedDuringRun; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 168; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1366 689; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #252504182988083449 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #252504182988083449; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; getTable; tell It; rowNamesWidth 130; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1198 622; setLocation -8 -8; 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 #252504182988083449 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 933.1339531087363.513679754849170597; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1198 622; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; 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 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; 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 #1019131953878553712 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1198 622; 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;