#NEXUS [written Tue Jun 12 14:22:41 CST 2012 by Mesquite version 2.75 (build 564) at YuIto-PC/10.226.147.91] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=9; TAXLABELS Ruppia_maritima_B Ruppia_maritima_D Ruppia_maritima_F 'Ruppia maritima B''''''' Ruppia_maritima_E Ruppia_cirrhosa_JN113271 'Ruppia maritima B''' Ruppia_maritima_C Ruppia_cirrhosa_JN113272 ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=452; FORMAT DATATYPE = DNA INTERLEAVE GAP = - MISSING = -; MATRIX Ruppia_maritima_B ACAACTTCCCTCTAGACCTGGCTGCTGTTGAAGTTCCATCTATAAACGGATAAGACTTTTTTTTATTATAGTGTATATATATACGAATAAAAATCGTTGA Ruppia_maritima_D ACAACTTCCCTCTAGACCTGGCTGCTGTTGAAGTTCCATCTATAAACGGATAAGACTTTTTTTTATTATAGTGTATATATATACGAATAAAAATCGTTGA Ruppia_maritima_F ACAACTTCCCTCTAGACCTGGCTGCTGTTGAAGTTCCATCTATAAACGGATAAGACTTTTTTTTATTATAGTGTATATATA--CGAATAAAAATCGTTGA 'Ruppia maritima B''''''' ACAACTTCCCTCTAGACCTGGCTGCTGTTGAAGTTCCATCTATAAACGGATAAGACTTTTTTTTATTATAGTGTATATATATACGAATAAAAATCGTTGA Ruppia_maritima_E ACAACTTCCCTCTAGACCTGGCTGCTGTTGAAGTTCCATCTATAAACGGATAAGACTTTTTTTTATTATAGTGTATATATA--CGAATAAAAATCGTTGA Ruppia_cirrhosa_JN113271 ACAACTTCCCTCTAGACCTGGCTGCTGTTGAAGTTCCATCTATAAACGGATAAGACTTCTTTTTATTATAGTGTATATATA--CGAATAAAAATCGTTGA 'Ruppia maritima B''' ACAACTTCCCTCTAGACCTGGCTGCTGTTGAAGTTCCATCTATAAACGGATAAGACTTTTTTTTATTATAGTGTATATATATACGAATAAAAATCGTTGA Ruppia_maritima_C ACAACTTCCCTCTAGACCTGGCTGCTGTTGAAGTTCCATCTATAAACGGATAAGACTTTTTTTTATTATAGTGTATATATATACGAATAAAAATCGTTGA Ruppia_cirrhosa_JN113272 ACAACTTCCCTCTAGACCTGGCTGCTGTTGAAGTTCCATCTATAAACGGATAAGACTTTTTTTTATTATAGTGTATATATATACGAATAAAAATCGTTGA Ruppia_maritima_B AGTAGAAATACTAAACCTATTTATAAAA------AAATAGGTTTAGTATTTCTATAGTTCTACTGTTGGCGGATTCCTTAATCTTTTGCACACATAAGTA Ruppia_maritima_D AGTAGAAATACTAAACCTATTGATAAAA------CAATAGGTTTAGTATTTCTATAGTTCTACTGTTGGCGGATTCCTTAATTTTTTGCACACATAAGTA Ruppia_maritima_F AGTAGAAATACTAAACCTATTG------TTTTATCAATAGGTTTAGTATTTCTATAGTTCTACTGTTGGCAGATTCCTTAATCTTTTGTACACATAAGTA 'Ruppia maritima B''''''' AGTAGAAATACTAAACCTATTGATAAAA------CAATAGGTTTAGTATTTCTATAGTTCTACTGTTGGCGGATTCCTTAATCTTTTGCACACATAAGTA Ruppia_maritima_E AGTAGAAATACTAAACCTATTG------TTTTATCAATAGGTTTAGTATTTCTATAGTTCTACTGTTGGCAGATTTCTTAATCTTTTGTACACATAAGTA Ruppia_cirrhosa_JN113271 AGTAGAAATACTAAACCTATTG------TTTTATCAATAGGTTTAGTATTTCTATAGTTCTACTGTTGGCAGATTTCTTAATCTTTTGTACACATAAGTA 'Ruppia maritima B''' AGTAGAAATACTAAACCTATTGATAAAA------AAATAGGTTTAGTATTTCTATAGTTCTACTGTTGGCGGATTCCTTAATCTTTTGCACACATAAGTA Ruppia_maritima_C AGTAGAAATACTAAACCTATTGATAAAA------CAATAGGTTTAGTATTTCTATAGTTCTACTGTTGGCGGATTCCTTAATTTTTTGCACACATAAGTA Ruppia_cirrhosa_JN113272 AGTAGAAATACTAAACCTATTGATAAAA------CAATAGGTTTAGTATTTCTATAGTTCTACTGTTGGCGGATTCCTTAATTTTTTGCACACATAAGTA Ruppia_maritima_B TTTTTCATTTCATTTCTAA-----AATTGAGATATTCTTTTAAT-----AGATCACTCAAAGTAAAAAAGACTAAATAAAATAATGAATGATGCATGTAA Ruppia_maritima_D TTTTTCATTTCATTTCTAA-----AATTGAGATATTCTTTTAAT-----AGATCACTCAAAGTAAAAAAGACTAAATAAAATAATGAATGATGCATGTAA Ruppia_maritima_F TTTTTCATTTCATTTATAA-----AATTGAGATATTCTTTTAATATAATAGATCATTCAAAGTAAAAAAGACTAAATAAAATAATGAATGATGCATGTAA 'Ruppia maritima B''''''' TTTTTCATTTCATTTCTAATCTAAAATTGAGATATTCTTTTAAT-----AGATCACTCAAAGTAAAAAAGACTAAATAAAATAATGAATGATGCATGTAA Ruppia_maritima_E TTTTTCATTTCATTTATAA-----AATTGAGATATTCTTTTAATATAATAGATCATTCAAAGTAAAAAAAACTAAATAAAATAATGAATGATGCATGTAA Ruppia_cirrhosa_JN113271 TTTTTCATTTCATTTATAA-----AATTGAGA-----TTTTAATATAATAGATCATTCAAAGTAAAAAAAACTAAATAAAATAATGAATGATGCATGTAA 'Ruppia maritima B''' TTTTTCATTTCATTTCTAA-----AATTGAGATATTCTTTTAAT-----AGATCACTCAAAGTAAAAAAGACTAAATAAAATAATGAATGATGCATGTAA Ruppia_maritima_C TTTTTCATTTCATTTCTAA-----AATTGAGATATTCTTTTAAT-----AGATCACTCAAAGTAAAAAAGACTAAATAAAATAATGAATGATGCATGTAA Ruppia_cirrhosa_JN113272 TTTTTCATTTCATTTCTAA-----AATTGAGATATTCTTTTAAT-----AGATCACTCAAAGTAAAAAAGACTAAATAAAATAATGAATGATGCATGTAA Ruppia_maritima_B AAAAAT--------TTTAACTTAATAAATAGAAACTCATATTA--------------------TAAAATTTAATAT-----AAATAGATAAAATTGAATT Ruppia_maritima_D AAAAATAAAAAAATTTTAACTTAATAAATAGAAACTCATATTA--------------------TAAAATTTAATATAATATAAATAGATAAAATTGAATT Ruppia_maritima_F AAAAAT--------TTTAACTTAATAAATAGAAACTCATATTA--------------------TAAAATTTAATAT-----AAATAGATAAAATTGAATT 'Ruppia maritima B''''''' AAAAAT--------TTTAACTTAATAAATAGAAACTCATATTA--------------------TAAAATTTAATAT-----AAATAGATAAAATTGAATT Ruppia_maritima_E AAAAAT--------TTTAACTTAATAAATAGAAACTCATATTA--------------------TAAAATTTAATAT-----AAATAGATAAAATTGAATT Ruppia_cirrhosa_JN113271 AAAAAT--------TTTAACTTAATAAATAGAAACTCATATTA--------------------TAAAATTTAATAT-----AAATAGATAAAATTGAATT 'Ruppia maritima B''' AAAAAT--------TTTAACTTAATAAATAGAAACTCATATTA--------------------TAAAATTTAATAT-----AAATAGATAAAATTGAATT Ruppia_maritima_C AAAAATAAAAAAATTTTAACTTAATAAATAGAAACTCATATTA--------------------TAAAATTTAATAT-----AAATAGATAAAATTGAATT Ruppia_cirrhosa_JN113272 AAAAATAAAAAAATTTTAACTTAATAAATAGAAACTCATATTAATAAATAGAAACTCATATTATAAAATTTAATAT-----AAATAGATAAAATTGAATT Ruppia_maritima_B ATGATGCGATGTAAGTTAAGGGGCGGATGTAGCCAAGTGGATCAAGGCAGTG Ruppia_maritima_D ATGATGCGATGTAAGTTAAGGGGCGGATGTAGCCAAGTGGATCAAGGCAGTG Ruppia_maritima_F ATGATGCGATGTAAGTTAAGGGGCGGATGTAGCCAAGTGGATCAAGGCAGTG 'Ruppia maritima B''''''' ATGATGCGATGTAAGTTAAGGGGCGGATGTAGCCAAGTGGATCAAGGCAGTG Ruppia_maritima_E ATGATGCGATGTAAGTTAAGGGGCGGATGTAGCCAAGTGGATCAAGGCAGTG Ruppia_cirrhosa_JN113271 ATGATGCGATGTAAGTTAAGGGGCGGATGTAGCCAAGTGGATCAAGGCAGTG 'Ruppia maritima B''' ATGATGCGATGTAAGTTAAGGGGCGGATGTAGCCAAGTGGATCAAGGCAGTG Ruppia_maritima_C ATGATGCGATGTAAGTTAAGGGGCGGATGTAGCCAAGTGGATCAAGGCAGTG Ruppia_cirrhosa_JN113272 ATGATGCGATGTAAGTTAAGGGGCGGATGTAGCCAAGTGGATCAAGGCAGTG ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 452; END; BEGIN TREES; Title 'Trees from "Ruppia_psbAtrnH..tre"'; LINK Taxa = Taxa; TRANSLATE 1 Ruppia_maritima_B, 2 Ruppia_maritima_D, 3 Ruppia_maritima_F, 4 'Ruppia maritima B''''''', 5 Ruppia_maritima_E, 6 Ruppia_cirrhosa_JN113271, 7 'Ruppia maritima B''', 8 Ruppia_maritima_C, 9 Ruppia_cirrhosa_JN113272; TREE PAUP_1 = (((1:1.0,7:0.0):1.0,(2:1.0,8:0.0,9:1.0):2.0,4:1.0):0.0,(3:0.0,(5:0.0,6:2.0):2.0):8.0); END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 452; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 452; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1339532561583; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 2994082469825375824; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 4943148926638221994; mqVersion 275; checksumv 0 3 934092125 null getNumChars 452 numChars 452 getNumTaxa 9 numTaxa 9 short true bits 15 states 15 sumSquaresStatesOnly 93643.0 sumSquares 93643.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 168; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 700 464; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #2994082469825375824 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #2994082469825375824; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 532 397; 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 #2994082469825375824 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 838.1339532542758.9107135881781762050; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 532 397; 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; endTell; end;