#NEXUS [written Fri Aug 24 15:26:53 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_EU1 Phytophthora_ramorum_NA1 Phytophthora_ramorum_NA2 Phytophthora_ramorum_EU2 Phytophthora_lateralis Phytophthora_hibernalis ; END; BEGIN CHARACTERS; TITLE alignment_Cox2; DIMENSIONS NCHAR=922; FORMAT DATATYPE = DNA INTERLEAVE GAP = - MISSING = ?; MATRIX Phytophthora_ramorum_EU1 ATGGAAGGTATTATTAACTTTCACCATGATTTAATGTTTTTTTTAATTATGATTACTGTATTTGTTTGTTGGATGTTATTTAGAGTTATTACTCTTTTT Phytophthora_ramorum_NA1 ATGGAAGGTATTATTAACTTTCACCATGATTTAATGTTTTTTTTAATTATGATTACTGTATTTGTTTGTTGGATGTTATTTAGAGTTATTACTCTTTTT Phytophthora_ramorum_NA2 ATGGAAGGTATTATTAACTTTCACCATGATTTAATGTTTTTTTTAATTATGATTACTGTATTTGTTTGTTGGATGTTATTTAGAGTTATTACTCTTTTT Phytophthora_ramorum_EU2 ATGGAAGGTATTATTAACTTTCACCATGATTTAATGTTTTTTTTAATTATGATTACTGTATTTGTTTGTTGGATGTTATTTAGAGTTATTACTCTTTTT Phytophthora_lateralis ATGGAAGGTATTATTAATTTTCACCACGATTTGATGTTTTTTTTAATAATGATTACCGTATTTGTTTGTTGGATGTTATTTAGAGTTATTACTCTTTTT Phytophthora_hibernalis ATGGAAGGTATTATTAACTTTCATCATGATTTAATGTTTTTTTTAATTATGATTACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACTCTTTTT Phytophthora_ramorum_EU1 GATGAAAAAAAAAATAAAATTCCTTCAACGGTAGTACATGGAGCTACTATTGAAATTATTTGGACATCTATTCCAGCTTTAATTTTATTAGTTGTTGCA Phytophthora_ramorum_NA1 GATGAAAAAAAAAATAAAATTCCTTCAACGGTAGTACATGGAGCTACTATTGAAATTATTTGGACATCTATTCCAGCTTTAATTTTATTAGTTGTTGCA Phytophthora_ramorum_NA2 GATGAAAAAAAAAATAAAATTCCTTCAACGGTAGTACATGGCGCTACTATTGAAATTATTTGGACATCTATTCCAGCTTTAATTTTATTAGTTGTTGCA Phytophthora_ramorum_EU2 GATGAAAAAAAAAATAAAATTCCATCAACGGTAGTACATGGAGCTACTATTGAAATTATTTGGACATCTATTCCAGCTTTAATTTTATTAGTTGTTGCA Phytophthora_lateralis GATGAAAACAAAAACAAAAACGCATCAACAGTTGTGCATGGAGCTACTATCGAAATTATTTGGACTTCTATTCCAGCTTTAATTTTATTAGTTGTTGCA Phytophthora_hibernalis GATGAAAAAAAAAATAAGATTCCATCAACTGTAGTACACGGGGCTACTATTGAAATTATTTGGACATCTATTCCAGCTTTAATTTTATTAATTGTAGCA Phytophthora_ramorum_EU1 GTACCATCTTTTGCTTTATTATATTCAATGGATGAGGTAATTGATCCAATTATTACATTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATAT Phytophthora_ramorum_NA1 GTACCATCTTTTGCTTTATTATATTCAATGGATGAGGTAATTGATCCAATTATTACATTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATAT Phytophthora_ramorum_NA2 GTACCATCTTTTGCTTTATTATATTCAATGGATGAGGTAATTGATCCAATTATTACATTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATAT Phytophthora_ramorum_EU2 GTACCATCTTTTGCTTTATTATATTCAATGGATGAGGTAATTGATCCAATTATTACATTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATAT Phytophthora_lateralis GTTCCCTCTTTTGCTTTATTATATTCGATGGATGAAGTTATTGACCCAATTATTACGTTAAAAGTGATTGGTAGTCAATGGTACTGGAGTTATGAATAT Phytophthora_hibernalis GTTCCATCTTTTGCTTTATTATATTCAATGGATGAAGTAATTGATCCTATTATTACTTTAAAAGTAATTGGAAGTCAATGGTACTGGAGTTATGAATAT Phytophthora_ramorum_EU1 TCTGATAATTTAGAATTTTCTGATGAACCTTTAATTTTTGATAGTTACATGATACAAGAAGATGATTTAGCAATAGGTCAATTTAGAGTTTTAGAAGTA Phytophthora_ramorum_NA1 TCTGATAATTTAGAATTTTCTGATGAACCTTTAATTTTTGATAGTTACATGATACAAGAAGATGATTTAGCAATAGGTCAATTTAGAGTTTTAGAAGTA Phytophthora_ramorum_NA2 TCTGATAATTTAGAATTTTCTGATGAACCTTTAATTTTTGATAGTTACATGATACAAGAAGATGATTTAGCAATAGGTCAATTTAGAGTTTTAGAAGTA Phytophthora_ramorum_EU2 TCTGATAATTTAGAATTTTCTGATGAACCTTTAATTTTTGATAGTTACATGATACAAGAAGATGATTTAGCAATAGGTCAATTTAGAGTTTTAGAAGTA Phytophthora_lateralis TCCGATAATTTGGAATTTTCGGATGAACCTTTAATTTTTGATAGTTATATGTTACAAGAAGAAGATTTAGCTATAGGTCAATTCAGAGTTTTAGAAGTG Phytophthora_hibernalis TCAGATAATTTAGAATTTTCGGATGAACCTTTAATTTTTGATAGTTACATGATACAAGAAGATGATTTAGCAATAGGACAATTTAGGGTTTTAGAAGTA Phytophthora_ramorum_EU1 GATAATCGTGTAGTTGTACCAACAAATAGTCATATTAGAGTATTAATTACCGCATCAGATGTTTTACATTCATGGGCTATTCCTTCATTAGGTATTAAA Phytophthora_ramorum_NA1 GATAATCGTGTAGTTGTACCAACAAATAGTCATATTAGAGTATTAATTACCGCATCAGATGTTTTACATTCATGGGCTATTCCTTCATTAGGTATTAAA Phytophthora_ramorum_NA2 GATAATCGTGTAGTTGTACCAACAAATAGTCATATTAGAGTATTAATTACCGCATCAGATGTTTTACATTCATGGGCTATTCCTTCATTAGGTATTAAA Phytophthora_ramorum_EU2 GATAATCGTGTAGTTGTACCAACAAATAGTCATATTAGAGTATTAATTACCGCATCAGATGTTTTACATTCATGGGCTATTCCTTCATTAGGTATTAAA Phytophthora_lateralis GATAATCGTGTAGTGGTACCAACTAATAGTCATATTAGAGTATTAATTACAGCATCCGATGTTTTACATTCATGGGCTATTCCCTCATTAGGTATTAAA Phytophthora_hibernalis GATAATCGTGTAGTAGTACCTACAAATAGTCATATTAGAGTATTAATTACGGCATCAGATGTTTTACATTCTTGGGCTATACCATCATTAGGTATAAAA Phytophthora_ramorum_EU1 TTAGATGCATGTCCTGGACGTTTAAATCAAACATCAATGTTTATTAAAAGAGAAGGTGTTTTTTATGGACAATGTAGTGAAATTTGTGGAGTAAATCAT Phytophthora_ramorum_NA1 TTAGATGCATGTCCTGGACGTTTAAATCAAACATCAATGTTTATTAAAAGAGAAGGTGTTTTTTATGGACAATGTAGTGAAATTTGTGGAGTAAATCAT Phytophthora_ramorum_NA2 TTAGATGCATGTCCTGGACGTTTAAATCAAACATCAATGTTTATTAAAAGAGAAGGTGTTTTTTATGGACAATGTAGTGAAATTTGTGGAGTAAATCAT Phytophthora_ramorum_EU2 TTAGATGCATGTCCAGGACGTTTAAATCAAACATCAATGTTTATTAAAAGAGAAGGTGTTTTTTATGGACAATGTAGTGAAATTTGTGGAGTAAATCAT Phytophthora_lateralis TTAGATGCTTGTCCTGGACGTTTAAATCAAACATCAATGTTTATTAAAAGGGAAGGTGTTTTTTATGGACAATGTAGTGAAATTTGTGGAGTAAATCAC Phytophthora_hibernalis TTGGATGCATGTCCTGGACGTTTAAATCAAACATCTATGTTTATTAAAAGAGAGGGTGTTTTTTATGGACAATGTAGCGAAATTTGTGGAGTAAATCAT Phytophthora_ramorum_EU1 GGATTTATGCCTATTGTTGTAGAAGCTGTTTCATTAGAAGATTATTTAACTTGGTTAAAAAATAAAATCAATTTTGATTTTAATGTATAATGATTTTAA Phytophthora_ramorum_NA1 GGATTTATGCCTATTGTTGTAGAAGCTGTTTCATTAGAAGATTATTTAACTTGGTTAAAAAATAAAATCAATTTTGATTTTAATGTATAATGATTTTAA Phytophthora_ramorum_NA2 GGATTTATGCCTATTGTTGTAGAAGCTGTTTCATTAGAAGATTATTTAACTTGGTTAAAAAATAAAATCAATTTTGATTTTAATGTATAATGATTTTAA Phytophthora_ramorum_EU2 GGATTTATGCCTATTGTTGTAGAAGCTGTTTCATTAGAAGATTATTTAACTTGGTTAAAAAATAAAATCAATTTTG----------------ATTTTAA Phytophthora_lateralis GGATTTATGCCTATTGTTGTAGAAGCTGTTTCATTAGAAGATTATTTAACATGGTTAAAAAATAAAATCAATTTTG----------------ATTTTAA Phytophthora_hibernalis GGATTTATGCCGATTGTTGTAGAAGCTGTTTCATTAGAAGATTATTTAACTTGGTTAAAAAATAAAATAAATTTTG----------------ATTTTAA Phytophthora_ramorum_EU1 TGTATAATTAAATTAATTTTATGGTATTTAAAATCATAGGTGTAATTTGTTTAATATTATTATTATTTACAGATATTAAACAAATTATATATAAAATCA Phytophthora_ramorum_NA1 TGTATAATTAAATTAATTTTATGGTATTTAAAATCATAGGTGTAATTTGTTTAATATTATTATTATTTACAGATATTAAACAAATTATATATAAAATCA Phytophthora_ramorum_NA2 TGTATAATTAAATTAATTTTATGGTATTTAAAATCATGGGTGTAATTTGTTTAATATTATTATTATTTACAGATATTAAACAAATTATATATAAAATCA Phytophthora_ramorum_EU2 TGTATAATTAAATTAATTTTATGGTATTTAAAATCATGGGTGTAATTTGTTTAATATTATTATTATTTACAGATATTAAACAAATTATATATAAAATCA Phytophthora_lateralis TGTATAATTAAAGTAATTTTATGGTATTTAAAATCATTGGTATAATTTTTTTAATATTATTATTATTTACAGATATTAAACAAATTATAAATAAAATTA Phytophthora_hibernalis TATATAAT------AATTTTATGATATTTAAAATAATTGGTATAATTTTTTTAATATTATTATTATTTACTGATATTAAAAAAATAATAAATAAAATTA Phytophthora_ramorum_EU1 AACAATTTTTTAATAAATAAAAAAA----TATTATCATTGATAATATAAATT-AAAAAAACCAACGCTTTTTTTAATTAAAAAAA--TATATAATTTTG Phytophthora_ramorum_NA1 AACAATTTTTTAATAAATAAAAAAA----TATTATCATTGATAATATAAATT-AAAAAAACCAACGCTTTTTTTAATTAAAAAAA--TATATAATTTTG Phytophthora_ramorum_NA2 AACAATTTTTTAATAAATAAAAAAA----TATTATCAATGATAATATAAATT-AAAAAAACCAACGCTTTTTTTAATTAAAAAAA--TATATAATTTTG Phytophthora_ramorum_EU2 AACAATTTTTTAATAAATAAAAAAA----TATTATCATTGATAATATAAATT-AAAAAAACCAACGCTTTTTTTAATTAAAAAAA--TATATAATTTTG Phytophthora_lateralis AACAATTTTTTAATAAATACTAAAAAG--TATTATTAT---TAATCCAAATTTAAAAAAACCAACGCTTTTTTTAATTAAAAAAA--TATATAATTTTG Phytophthora_hibernalis AACAATTCTTTAATAAATAAAAAATAAACTATTATCTAGTATAATATAAATT-AAAAAAACCAACGCTTTTTTTAATTAAAAAAAAATATATAATTTTG Phytophthora_ramorum_EU1 CATTTAAATTAAATTTTAAAAATATTCAAAA Phytophthora_ramorum_NA1 CATTTAAATTAAATTTTAAAAATATTCAAAA Phytophthora_ramorum_NA2 CATTTAAATTAAATTTTAAAAATATTCAAAA Phytophthora_ramorum_EU2 CATTTAAATTAAATTTTAAAAATATTCAAAA Phytophthora_lateralis CATTTAAACCGAATTTAAAAAATATTTAAAA Phytophthora_hibernalis CATTTAAATTAAAATTTAAAAATATTCAAAA ; END; BEGIN TREES; Title tree_Cox2; LINK Taxa = Taxa; TRANSLATE 1 Phytophthora_ramorum_EU1, 2 Phytophthora_ramorum_NA1, 3 Phytophthora_ramorum_NA2, 4 Phytophthora_ramorum_EU2, 5 Phytophthora_lateralis, 6 Phytophthora_hibernalis; TREE Imported_tree_0 = ((((1:0.0,2:0.0)0.7010:0.00117873,3:0.0023725)0.4100:0.00118196,4:0.00118549)0.3250:0.0100093,6:0.0594562,5:0.07229674); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 922; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 922; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 922; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1345814813976; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 3270919197599276136; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 8721731712757155112; mqVersion 275; checksumv 0 3 3360938659 null getNumChars 922 numChars 922 getNumTaxa 6 numTaxa 6 short true bits 15 states 15 sumSquaresStatesOnly 156858.0 sumSquares 156858.0 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 1762 682; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #3270919197599276136 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 5329.1345799895218.52336870964040487; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1662 615; 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 '(((((1:0.0,2:0.0)0.7010:0.00117873,3:0.0023725)0.4100:0.00118196,4:0.00118549)0.3250:0.0100093,6:0.0594562):0.03614837,5:0.03614837);'; 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 #8721731712757155112 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 142; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1662 615; 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;