#NEXUS [written Fri Aug 24 15:37:36 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_Prv11; DIMENSIONS NCHAR=305; FORMAT DATATYPE = DNA INTERLEAVE GAP = - MISSING = ?; MATRIX Phytophthora_ramorum_EU2 AAAAGGATGTCGATTTGTTTCAGCTAAACATGATATAAAAAAAATTAAAAAAATGGGAAAAAGTGGAAAACAATACCATACAGTTTTTTGTGCTAATAC Phytophthora_ramorum_EU1 AAAAGGATGTCGATTTGTTTCAGCTAAACATGATATAAAAAAAATTAAAAAAATGGGAAAAAGTGGAAAACAATACCATATAGTTTTTTGTGCTAATAC Phytophthora_ramorum_NA1 AAAAGGATGTCGATTTGTTTCAGCTAAACATGATATAAAAAAAATTAAAAAAATGGGAAAAAGTGGAAAACAATACCATACAGTTTTTTGTGCTAATAC Phytophthora_ramorum_NA2 AAAAGGATGTCGATTTGTTTCAGCTAAACATGATATAAAAAAAATTAAAAAAATGGGAAAAAGTGGAAAACAATACCATACAGTTTTTTGTGCTAATAC Phytophthora_lateralis GAATGGATGTCGATTAGTTTCAGCTAAACATGATATAAAAAAAATTAAAAAAATAGGAAAAAGAGGAAAACAATACCATACGGTTTTTTGAGCTAATAC Phytophthora_hibernalis GAAGGGATGTCTATTAGTTTCAGCTAAACATGAAATAAAAAAAATTAACAAAATAGGAAAAAGAGGAAAACAATACCATACTGTTTTTTGTGCTAATAC Phytophthora_ramorum_EU2 TATTGAAATTAAATTTAAAGATTTCGCACAAACTATTACAGAAAGAATAGAAAATCCAATTGTTAATTCATAAGAAATCATTTGTGCAGTTGATCTTAA Phytophthora_ramorum_EU1 TATTGAAATTAAATTTAAAGATTTTGCACAAACTATTACAGAAAGAATAGAAAATCCAATTGTTAATTCATAAGAAATCATTTGTGCAGTTGATCTTAA Phytophthora_ramorum_NA1 TATTGAAATTAAATTTAAAGATTTTGCACAAACTATTACAGAAAGAATAGAAAATCCAATTGTTAATTCATAAGAAATCATTTGTGCAGTTGATCTTAA Phytophthora_ramorum_NA2 TATTGAAATTAAATTTAAAGATTTTGCACAAACTATTACAGAAAGAATAGAAAATCCAATTGTTAATTCATAAGAAATCATTTGTGCAGTTGATCTTAA Phytophthora_lateralis TATAGAAATTAAGTTTAAAGATTTAGCACAAACAATTACAGAAAGAATAGAAAATCCAATCGTTAATTCATAAGAAATCATTTGTGCAGTTGATCTTAA Phytophthora_hibernalis TATCGAAATCAAATTTAACGACTTAGCACAAACAATTACAGAAAGAATTGAAAATCCAATAGTTAATTCATAAGAAATCATTTGAGCTGTAGATCTTAA Phytophthora_ramorum_EU2 AGCACCTAAAAAAGAATATTTAGAATTACTAGACCAACCACCAATAATAATACCATAAACACCTAATGATGAGATTGCTAATAAATATAAAATACCAAT Phytophthora_ramorum_EU1 AGCACCTAAAAAAGAATATTTAGAATTACTAGACCAACCACCAATAATAATACCATAAACACCTAATGATGAGATTGCTAATAAATATAAAATACCTAT Phytophthora_ramorum_NA1 AGCACCTAAAAAAGAATATTTAGAATTACTAGACCAACCACCAATAATAATACCATAAACACCTAATGATGAGATTGCTAATAAATATAAAATACCTAT Phytophthora_ramorum_NA2 AGCACCTAAAAAAGAATATTTAGAATTACTAGACCAACCACCAATAATAATACCATAAACACCTAATGATGAGATTGCTAATAAATATAAAATACCAAT Phytophthora_lateralis TGCACCTAAAAAGGAATATTTTGAATTACTTGACCAACCACCAATAATAATACCATAAACACCTAATGATGAAATTGCTAATAAATATAAAATACCTAT Phytophthora_hibernalis TGCACCTAAAAAAGAATATTTAGAATTACTAGACCAACCTCCAATAATAATACCATAAACCCCTAATGATGATATTGCTAATAAATATAAAATACCTAT Phytophthora_ramorum_EU2 ATTTAATT Phytophthora_ramorum_EU1 ATTTAATT Phytophthora_ramorum_NA1 ATTTAATT Phytophthora_ramorum_NA2 ATTTAATT Phytophthora_lateralis ATTTAATT Phytophthora_hibernalis ATTTAATT ; END; BEGIN TREES; Title tree_Prv11; 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 = (((1:0.00360542,4:6.05E-6)0.6530:0.00332388,(2:0.00363073,3:0.0)0.4370:0.00306811)0.9530:0.04569403,5:0.02983953,6:0.07744255); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 305; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 305; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 305; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1345815456786; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 5628268056431633370; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 3758521860024579834; mqVersion 275; checksumv 0 3 1641902826 null getNumChars 305 numChars 305 getNumTaxa 6 numTaxa 6 short true bits 15 states 15 sumSquaresStatesOnly 39243.0 sumSquares 39243.0 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 1673 490; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #5628268056431633370 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 6009.1345800474533.5297700848449168047; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1573 423; 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 '((((1:0.00360542,4:6.05E-6)0.6530:0.00332388,(2:0.00363073,3:0.0)0.4370:0.00306811)0.9530:0.04569403,5:0.02983953):0.038721275,6:0.038721275);'; 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 #3758521860024579834 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1573 423; 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; getWindow; tell It; forceAutosize; endTell; hideWindow; 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;