#NEXUS [written Fri Aug 24 15:25:17 CEST 2012 by Mesquite version 2.75 (build 564) at P96lKrisVP/192.168.250.193] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=6; TAXLABELS Phytophthora_ramorum_EU2 Phytophthora_ramorum_EU1 Phytophthora_ramorum_NA1 Phytophthora_ramorum_NA2 Phytophthora_lateralis Phytophthora_hibernalis ; END; BEGIN CHARACTERS; TITLE alignment_Cox1; DIMENSIONS NCHAR=425; FORMAT DATATYPE = DNA INTERLEAVE GAP = - MISSING = ?; MATRIX Phytophthora_ramorum_EU2 TAGATACTCGAGCTTATTTTTCTGCAGCTACTATGATTATTGCTGTACCTACAGGTATTAAAATTTTTAGTTGGTTAGCTACTTTATGGGGTGGTTCAT Phytophthora_ramorum_EU1 TAGATACTAGAGCTTATTTTTCTGCAGCTACTATGATTATTGCTGTACCTACAGGTATTAAAATTTTTAGTTGGTTAGCTACTTTATGGGGTGGTTCAT Phytophthora_ramorum_NA1 TAGATACTAGAGCTTATTTTTCTGCAGCTACTATGATTATTGCTGTACCTACAGGTATTAAAATTTTTAGTTGGTTAGCTACTTTATGGGGTGGTTCAT Phytophthora_ramorum_NA2 TAGATACTCGAGCTTATTTTTCTGCAGCTACTATGATTATTGCTGTACCTACAGGTATTAAAATTTTTAGTTGGTTAGCTACCTTATGGGGTGGTTCAT Phytophthora_lateralis TAGATACTCGAGCTTATTTTTCTGCAGCAACTATGATTATTGCGGTACCTACAGGTATTAAAATCTTTAGTTGGTTAGCAACTTTATGGGGAGGTTCTT Phytophthora_hibernalis TAGATACTCGAGCTTATTTTTCTGCAGCTACTATGATTATAGCGGTACCTACCGGTATTAAAATTTTTAGTTGGTTAGCTACTTTATGGGGCGGTTCAT Phytophthora_ramorum_EU2 TAAAATTTGAAACACCTTTATTATTTACCTTAGGTTTTATTTTATTATTTGTTATGGGTGGAGTAACTGGTGTGGCTATGTCTAATTCAGGTTTAGATA Phytophthora_ramorum_EU1 TAAAATTTGAAACACCTTTATTATTTACCTTAGGTTTTATTTTATTATTTGTTATGGGTGGAGTAACAGGTGTGGCTATGTCTAATTCAGGTTTAGATA Phytophthora_ramorum_NA1 TAAAATTTGAAACACCTTTATTATTTACCTTAGGTTTTATTTTATTATTTGTTATGGGTGGAGTAACAGGTGTGGCTATGTCTAATTCAGGTTTAGATA Phytophthora_ramorum_NA2 TAAAATTTGAAACACCTTTATTATTTACCTTAGGTTTTATTTTATTATTTGTTATGGGTGGAGTAACAGGTGTGGCTATGTCTAATTCAGGTTTAGATA Phytophthora_lateralis TAAAATTTGAAACACCTTTATTATTTACATTAGGTTTTATTTTATTATTCGTTATGGGTGGTGTAACTGGTGTAGCTATGTCTAATTCTGGTTTAGATA Phytophthora_hibernalis TAAAATTTGAAACACCTTTATTATTTACTTTAGGTTTTATTTTATTATTTGTTATGGGTGGTGTAACTGGTGTGGTTATGTCTAATTCGGGTTTAGATA Phytophthora_ramorum_EU2 TTGCATTACATGATACTTATTATATTGTAGGACATTTTCATTATGTATTATCTATGGGTGCTGTATTTGGTATCTTTACTGGATTTTATTTTTGGATTG Phytophthora_ramorum_EU1 TTGCATTACATGATACTTATTATATTGTAGGACATTTCCATTATGTATTATCTATGGGTGCTGTATTTGGTATCTTTACTGGATTTTATTTTTGGATTG Phytophthora_ramorum_NA1 TTGCATTACATGATACTTATTATATTGTAGGACATTTCCATTATGTATTATCTATGGGTGCTGTATTTGGTATCTTTACTGGATTTTATTTTTGGATTG Phytophthora_ramorum_NA2 TTGCATTACATGATACTTATTATATTGTAGGACATTTCCATTATGTATTATCTATGGGTGCTGTATTTGGTATCTTTACTGGATTTTATTTTTGGATTG Phytophthora_lateralis TTGCATTACATGATACTTATTATATTGTAGGACACTTTCATTATGTATTATCTATGGGAGCTGTTTTTGGTATTTTTACTGGACTTTATTTTTGGATTG Phytophthora_hibernalis TTGCATTACACGATACTTATTATATTGTAGGACATTTCCATTATGTATTATCTATGGGTGCTGTTTTTGGTATTTTTACAGGATTTTATTTTTGGATTG Phytophthora_ramorum_EU2 GAAAAATATCTGGTCGTAGATATCCTGAAATTTTAGGTCAAATTCATTTTTGGTTATTTTTTATTGGGGTAAATGTAACTTTTTTTCCTATGCATTTTT Phytophthora_ramorum_EU1 GAAAAATATCTGGTCGTAGATATCCTGAAATTTTAGGTCAAATCCATTTTTGGTTATTTTTTATTGGGGTAAATGTAACTTTTTTTCCTATGCATTTTT Phytophthora_ramorum_NA1 GAAAAATATCTGGTCGTAGATATCCTGAAATTTTAGGTCAAATTCATTTTTGGTTATTTTTTATTGGGGTAAATGTAACTTTTTTTCCTATGCATTTTT Phytophthora_ramorum_NA2 GAAAAATATCTGGTCGTAGATATCCTGAAATTTTAGGTCAAATTCATTTTTGGTTATTCTTTATTGGGGTAAATGTAACTTTTTTTCCTATGCATTTTT Phytophthora_lateralis GAAAAATATCTGGTCGTAGATATCCTGAAATTTTGGGTCAAATTCATTTTTGGTTATTCTTTATTGGGGTAAATGTAACTTTTTTTCCAATGCACTTTT Phytophthora_hibernalis GAAAAATATCTGGACGTAGATATCCTGAGATTTTAGGCCAAATTCATTTTTGGTTATTCTTTATTGGAGTAAATGTAACTTTTTTTCCTATGCATTTTT Phytophthora_ramorum_EU2 TAGGTCTAGCTGGTATGCCTAGAAGAATT Phytophthora_ramorum_EU1 TAGGTTTAGCTGGTATGCCTAGAAGAATT Phytophthora_ramorum_NA1 TAGGTTTAGCTGGTATGCCTAGAAGAATT Phytophthora_ramorum_NA2 TAGGTCTAGCTGGTATGCCTAGAAGAATT Phytophthora_lateralis TAGGTTTAGCTGGTATGCCTAGAAGAATT Phytophthora_hibernalis TAGGTTTAGCAGGTATGCCTAGAAGAATT ; END; BEGIN TREES; Title tree_Cox1; LINK Taxa = Taxa; TRANSLATE 1 Phytophthora_ramorum_EU2, 2 Phytophthora_ramorum_EU1, 3 Phytophthora_ramorum_NA1, 4 Phytophthora_ramorum_NA2, 5 Phytophthora_lateralis, 6 Phytophthora_hibernalis; TREE Imported_tree_0 = ((((2:0.00262307,3:0.0)0.8940:0.0065639,4:0.003889)0.5750:0.00349728,1:0.00293028)0.8070:0.01830041,6:0.04332709,5:0.0538494); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 425; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 425; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 425; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1345814718107; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8181002360050833248; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 1220018883763950623; mqVersion 275; checksumv 0 3 3419178938 null getNumChars 425 numChars 425 getNumTaxa 6 numTaxa 6 short true bits 15 states 15 sumSquaresStatesOnly 82617.0 sumSquares 82617.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1209 470; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #8181002360050833248 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 5034.1345799777332.585675269951038910; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1109 403; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.interchange; 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; 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 1; setTree '(((((2:0.00262307,3:0.0)0.8940:0.0065639,4:0.003889)0.5750:0.00349728,1:0.00293028)0.8070:0.01830041,6:0.04332709):0.0269247,5:0.0269247)<> <> < setBetweenBits = selected >;'; 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;