#NEXUS [written Tue Jun 12 16:12:10 CST 2012 by Mesquite version 2.75 (build 564) at YuIto-PC/10.226.157.92] 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 TTTCCGTAGGTGAACCTGCGGAAGGATCATTGTCGAGATGGATAGTAATAAACGAACACGTCACCGAATTATTTTGGAAGGGTGTGTTTTTGATGCACTTTATCCTAGCGGAAATGTTATGCTCCCTTTGGG--TGTGTGCATTTGTGCTTAACAACCAACCCTGGCACAACTTGTGTCAAGCAAAATGTAGCTTGTGGTTTGTCTCCTTCATTGTATTGAGATAGATCGTGAGTCTCCCAGAATTACCATTAAATGCATGACTCCCGTCAACGGATATCTTGGCCCTTGCATCGATGAAGAACGTAGCAAAATGCGATACTTGATGTGAATTGTAGAATCCCGTGAACCATCGAGTCTTTGAATGCAAGTTGCGCCCGAAGTTGTTAGACGGACGGCATGCCTGCCTGGGCGTCATTAAATGAGTCGCTCATTAAGTATGATCTTCATGGTTGATGAAGCGGATTTTGGCCTTCTGGGAGTTTTCCAGTAGGCTTAAATGGGCGTGACCTGCTGTGTGGAGATGCACGATGGGTGGTGAACATTTGTGAATTGCAGTTGATCCCATCATTAGCAAATAGCACGTCGTGCCTCCCGCAACACCTTCTTTCACGTGCTTACCCTTTGCATAAGGCATCTTGAGGATGCTTTGATTGAACAGTAGAGAATCTGACTGGGACCTCAGGTCAGGCAAGACCACCTGCTGAGTTTAA Ruppia_maritima_D TTTCCGTAGGTGAACCTGCGGAAGGATCATTGTCGAGATGGATAGTAATAAACGAACACGTCACCGAATTATTTTGGAAGAGTGTGTCTTTGATGCACTTTATCCTAGCGGAAATGTTACGCTCCCTTCGGG--TGTGTGCATTTGTGCTTAACAACCAACCCTGGCACAACTTGTGTCAAGCAAAATGTAGCTTGTGGTTTGTCTCCTTCATTGTATTGAGATAGATCGTGAGTCTCACAGAATTACCATTAAATGCATGACTCCCGTCAACGGATATCTTGGCCCTTGCATCGATGAAGAACGTAGCAAAATGCGATACTTGATGTGAATTGTAGAATCCCGTGAACCATCGAGTCTTTGAATGCAAGTTGCGCCCGAAGTTGTTAGACGGACGGCATGCCTGCCTGGGCGTCATTAAATGAGTCGCTCATTAAGTATGATCTTCATGGTTGATGAAGCGGATTTTGGCCTTCTGGGAGTTTTCCAGTAGGCTTAAATGGGCGTGACCTGCTGTGTGGAGATGCACGATGGGTGGTGAACATTTGTGAATTGCAGTTGATCCCATCATTAGCAAATAGCACGTCGTGCCTCCCTCAACACCTTCTTTCACGTGCTTACCCTTTGCATAAGGCATCTTGTGGATGCTTTGATTGAACAGTAGAGAATCTGATTGGGACCTCAGGTCAGGCAAGACCACCTGCTGAGTTTAA Ruppia_maritima_F TTTCCGTAGGTGAACCTGCGGAAGGATCATTGTCGAGATGGATAGCAATAGACGAACACGTCACCGAATTATTTTGGAAAAGTGTGTTTTTGATACACTATGTCCTAGCAGAAATGCTATGCTCCCTTTGGGCGTGTGTGCATTTGTGCTCAACAACCAACCCTGGCACAACTTGTGTCAAGCAAAAAGTAGCTTGTGGTTTGTCTCCTTCATCGTATTGAGA-GGATCGCGAGTCTCACAGAATTACTATTAAATGCACGACTCCCGTCAACGGATATCTTGGCCCTTGCATCGATGAAGAACGTAGCAAAATGCGATACTTGATGTGAATTGTAGAATCCCGTGAACCATCGAGTCTTTGAATGCAAGTTGCGCCCGAAGTTGTTAGACGGACGGCATGCCTGCCTGGGCGTCATTAATTGAGTCGCTCATTAAGTATGATCTTCATGGTTGATGAAGCGGATTATGGCCTTCTGGGAATTATCCGGTAGGCTTAAATGGGCGTGACCTGCTGTGTGGAGATGCACGATGGGTGGTGAACTTTTGTGGATTGTAGTCGATCCCATCATTAGCGAATAGCACGTCGTGCCTCCCTCAACATCTTCTTTCACGTGCTTACCCTTTGCATAAGGTGTCTCGTTGGTGCCTTAATTGAAAAGTAGAGAATCTGATTGGGACCTCAGGTCAGGCAAGACCACCTGCTGAGTTTAA Ruppia_maritima_E TTTCCGTAGGTGAACCTGCGGAAGGATCATTGTCGAGAT-TATAGTAATAAACGAACACGTCACCGAATTATTTTGGAAGAGTGTGTCTTTGATGCACTTTATCCTAGCGGAAATGTTACGCTCCCTTCGGG--TGTGTGCATTTGTGCTTAACAACCAACCCTGGCACAACTTGTGTCAAGCAAAATGTAGCTTGTGGTTTGTCTCCTTCATTGTATTGAGATAGATCGTGAGTCTCACAGAATTACCATTAAATGCATGACTCCCGTCAACGGATATCTTGGCCCTTGCATCGATGAAGAACGTAGCAAAATGCGATACTTGATGTGAATTGTAGAATCCCGTGAACCATCGAGTCTTTGAATGCAAGTTGCGCCCGAAGTTGTTAGACGGACGGCATGCCTGCCTGGGCGTCATTAAATGAGTCGCTCATTAAGTATGATCTTCATGGTTGATGAAGCGGATTTTGGCCTTCTGGGAGTTTTCCAGTAGGCTTAAATGGGCGTGACCTGCTGTGTGGAGATGCACGATGGGTGGTGAACATTTGTGAATTGCAGTTGATCCCATCATTAGCAAATAGCACGTCGTGCCTCCCTCAACACCTTCTTTCACGTGCTTACCCTTTGCATAAGGCATCTTGTGGATGCTTTGATTGAACAGTAGAGAATCTGATTGGGACCTCAGGTCAGGCAAGACCACCTGCTGAGTTTAA 'Ruppia maritima B''''''' TTTCCGTAGGTGAACCTGCGGAAGGATCATTGTCGAGATGGATAGTAATAAACGAACACGTCACCGAATTATTTTGGAAGAGTGTGTCTTTGATGCACTTTATCCTAGCGGAAATGTTACGCTCCCTTCGGG--TGTGTGCATTTGTGCTTAACAACCAACCCTGGCACAACTTGTGTCAAGCAAAATGTAGCTTGTGGTTTGTCTCCTTCATTGTATTGAGATAGATCGTGAGTCTCACAGAATTACCATTAAATGCATGACTCCCGTCAACGGATATCTTGGCCCTTGCATCGATGAAGAACGTAGCAAAATGCGATACTTGATGTGAATTGTAGAATCCCGTGAACCATCGAGTCTTTGAATGCAAGTTGCGCCCGAAGTTGTTAGACGGACGGCATGCCTGCCTGGGCGTCATTAAATGAGTCGCTCATTAAGTATGATCTTCATGGTTGATGAAGCGGATTTTGGCCTTCTGGGAGTTTTCCGGTAGGCTTAAATGGGCGTGACCTGCTGTGTGGAGATGCACGATGGGTGGTGAACATTTGTGAATTGCAGTTGATCCCATCATTAGCAAATAGCACGTCGTGCCTCCCTCAACGCCTTCTTTCACGTGCTTACCCTTTGCATAAGGCATCTTGTGGATGCTTTGATTGAACAGTAGAGAATCTGATTGGGACCTCAGGTCAGGCAAGACCACCTGCTGAGTTTAA 'Ruppia maritima E''' TTTCCGTAGGTGAACCTGCGGAAGGATCATTGTCGAGATGGATAGCAATAGACGAACACGTCACCGAATTATTTTGGAAAAGTGTGTTTTTGATGCACTTTGTCCTAGCAGAAATGCTATGCTCCCTTTGGGCGTGTGTGCATTTGTGCTCAACAACCAACCCTGGCACAACTTGTGTCAAGCAAAAAGTAGCTTGTGGTTTGTCTCCTTCATCGTATTGAGA-GGATCGCGAGTCTCACAGAATTACTATTAAATGCATGACTCCCGTCAACGGATATCTTGGCCCTTGCATCGATGAAGAACGTAGCAAAATGCGATACTTGATGTGAATTGTAGAATCCCGTGAACCATCGAGTCTTTGAATGCAAGTTGCGCCCGAAGTTGTTCGACGGACGGCATGCCTGCCTGGGCGTCATTAATTGAGTCGCTCATCAAGTATGATCTTCATGGTTGATGAAGCGGATTATGGCCTTCTGGGAATTATCCGGTAGGCTTAAATGGGCGTGACCTGCTGTGTGGAGATGCACGATGGGTGGTGAACTTTTGTGGATTGTAGTCGATCCCATCATTAGCGAATAGCACGTCGTGCCTCCCTCAACATCTTCTTTCACGTGCTTACCCTTTGCATAAGGTGTCTCGTTGGTGCCTTAATTGAAAAGTAGAGAATCTGATTGGGACCTCAGGTCAGGCAAGACCACCTGCTGAGTTTAA ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 712; END; BEGIN TREES; Title 'Trees from "Ruppia_ITS_Bayes.nex.con.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 con_50_majrule = (1:0.003704,(2:0.008318,(3:0.001353,5:0.004183,6:0.003757)0.95:0.00526)1.00:0.046578,(4:0.0053,7:0.004106)0.98:0.002635); TREE con_50_majrule = (1:0.003704,(2:0.008318,(3:0.001353,5:0.004183,6:0.003757):0.00526):0.046578,(4:0.0053,7:0.004106):0.002635); 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 1339539130398; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 4484131584054848805; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 5230336258335572460; mqVersion 275; checksumv 0 3 493136899 null getNumChars 712 numChars 712 getNumTaxa 7 numTaxa 7 short true bits 15 states 15 sumSquaresStatesOnly 118899.0 sumSquares 118899.0 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 700 464; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #4484131584054848805 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #4484131584054848805; 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; 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 #4484131584054848805 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1496.1339539042824.5562208686323031590; 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; setActive; 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;