#NEXUS [written Fri Aug 24 15:50:23 CEST 2012 by Mesquite version 2.75 (build 564) at P96lKrisVP/192.168.250.193] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=9; TAXLABELS Phytophthora_ramorum_EU2 Phytophthora_ramorum_NA1a Phytophthora_ramorum_NA1b Phytophthora_ramorum_NA2a Phytophthora_ramorum_NA2b Phytophthora_ramorum_EU1a Phytophthora_ramorum_EU1b Phytophthora_lateralis Phytophthora_hibernalis ; END; BEGIN CHARACTERS; TITLE alignment_gwEuk.30.30.1; DIMENSIONS NCHAR=664; FORMAT DATATYPE = DNA INTERLEAVE GAP = - MISSING = ?; MATRIX Phytophthora_ramorum_EU2 AGGACGTGGTGCTGGTGCTGCTGACGAATGGGTATCACAGCTCATCGTCGTCGGCCGGTGACTTTTTGAACAAAATTGAGGAATTTGCGGTAGAAGCCG Phytophthora_ramorum_NA1a AGGACGTGGTGCTGGTGCTGCTGACGAATGGGTATCACAGCTCATCGTCGTCGGCCGGTGACTTTTTGAACAAAATTGAGGAATTTGCGGTAGAAGCCG Phytophthora_ramorum_NA1b AGGACGTGGTGCTGGTGCTGCTGACGAATGGGTATCACAGCTCATCGTCGTCGGCCGGTGACTTTTTGAACAAAATTGAGGAATTTGCGGTAGAAGCCG Phytophthora_ramorum_NA2a AGGACGTGGTGCTGGTGCTGCTGACGAATGGGTATCACAGCTCATCGTCGTCGGCCGGTGACTTTTTGAACAAAATTGAGGAATTTGCGGTAGAAGCCG Phytophthora_ramorum_NA2b AGGACGTGGTGCTGGTGCTGCTGACGAATGGGTATCACAGCTCATCGTCGTCGGCCGGTGACTTTATGAACAAAATTGAGGAATTTGCGGTGGAAGCCG Phytophthora_ramorum_EU1a AGGACGTGGTGCTGGTGCTGCTGACGAATGGGTATCACAGCTCATCGTCGTCGGCCGGTGACTTTTTGAACAAAATTGAGGAATTTGCGGTAGAAGCCG Phytophthora_ramorum_EU1b AGGACGTGGTGCTGGTGCTGCTGACGAATGGGTATCACAGCTCATCGTCGTCGGCCGGTGACTTTATGAACAAAATTGAGGAATTTGCGGTGGAAGCCG Phytophthora_lateralis AGGACGTGGTGCTCGTGCTGCTGACGAATGGGTATCATAGCACATCGTCATCGGCCAGTGACTTTATGAACAACATTGAGGAGTTTGTGGTGGAAGCTG Phytophthora_hibernalis AGGATGTGGTGCTTGTGCTGCTGACGAATGGGTATCACAGCACGTCGTCGTCGGCCGGTGACTTTATGAACAATATTGAAAAGTTTGCGGTGGAAGCCG Phytophthora_ramorum_EU2 TGGGCAAGAAGCTTCATGAGCTGCCGCACCTTCACGTGTTGCCACCGCATATCCCGCAAGAGGCCATGCCGGCCTTGTACAAGGCTGCGAACGCGTTTG Phytophthora_ramorum_NA1a TGGGCAAGAAGCTTCATGAGCTGCCGCACCTTCACGTGTTGCCACCGCATATCCCGCAAGAGGCCATGCCGGCCTTGTACAAGGCTGCGAACGCGTTTG Phytophthora_ramorum_NA1b TGGGCAAGAAGCTTCATGAGCTGCCGCACCTTCACGTGTTGCCACCGCATATCCCGCAAGAGGCCATGCCGGCCTTGTACAAGGCTGCGAACGCGTTTG Phytophthora_ramorum_NA2a TGGGCAAGAAGCTTCATGAGCTGCCGCACCTTCACGTGTTGCCACCGCATATCCCGCAAGAGGCCATGCCGGCCTTGTACAAGGCTGCGAACGCGTTTG Phytophthora_ramorum_NA2b TGGGCAAGAAGCTGCATGAGCTGCCGCACCTTCACGTGTTACCACCGCATATCCCGCAAGAGGCCATGCCGGCCTTGTACAAGGCTGCGAACGCGTTTG Phytophthora_ramorum_EU1a TGGGCAAGAAGCTTCATGAGCTGCCGCACCTTCACGTGTTGCCACCGCATATCCCGCAAGAGGCCATGCCGGCCTTGTACAAGGCTGCGAACGCGTTTG Phytophthora_ramorum_EU1b TGGGCAAGAAGCTGCATGAGCTTCCGCACCTTCACGTGTTACCACCGCATATCCCGCAAGAGGCCATGCCGGCCTTGTACAAGGCTGCGAACGCGTTCG Phytophthora_lateralis TGGGCAAGAAGCTGCATGAACTGCCGCACCTTCACGTGTTGCCACCGCACATCCCGCAAGAGGCCATGCCTGCCCTGTACAAGGCTGCGAACGCGTTTG Phytophthora_hibernalis TGGGCAAGAAACTCAATGAGCTGCCTCACCTTCACGTGTTGCCACCGCACATCCCGCAAGAGGCGATGCTGGCATTGTATAAGGCTGCGAGCGCGTTTG Phytophthora_ramorum_EU2 TCCTGCCGTCGCGTGGCGAAGGATGGGGCCGACCGCATGTCGAGGCCATGGCCATGGAGCGGCCTGTGATTGCTACTTTTTGGAGCGGCACTACGGAAT Phytophthora_ramorum_NA1a TCCTGCCGTCGCGTGGCGAAGGATGGGGCCGACCGCATGTCGAGGCCATGGCCATGGAGCGGCCTGTGATTGCTACTTTTTGGAGCGGCACTACGGAAT Phytophthora_ramorum_NA1b TCCTGCCGTCGCGTGGCGAAGGGTGGGGCCGACCGCATGTCGAGGCCATGGCCATGGAGCGGCCTGTGATTGCTACTTTTTGGAGCGGCACTACGGAAT Phytophthora_ramorum_NA2a TCCTGCCGTCGCGTGGCGAAGGGTGGGGCCGACCGCATGTCGAGGCCATGGCCATGGAGCGGCCTGTGATTGCTACTTTTTGGAGCGGCACTACGGAAT Phytophthora_ramorum_NA2b TCCTGCCGTCGCGTGGCGAAGGGTGGGGCCGACCGCATGTCGAGGCCATGGCCATGGAGCGGCCTGTGATTGCTACTTTTTGGAGCGGCACTACGGAAT Phytophthora_ramorum_EU1a TCCTGCCGTCGCGTGGCGAAGGATGGGGCCGACCGCATGTCGAGGCCATGGCCATGGAGCGGCCTGTGATTGCTACTTTTTGGAGCGGCACTACGGAAT Phytophthora_ramorum_EU1b TCCTGCCGTCGCGTGGCGAAGGATGGGGCCGACCGCATGTCGAGGCCATGGCCATGGAGCGGCCTGTGATTGCTACTTTTTGGAGCGGCACTACGGAAT Phytophthora_lateralis TCCTGCCGTCGCGTGGTGAAGGATGGGGCCGACCGCATGTGGAGGCCATGGCGATGGAGCGGCCTGTGATTGCTACGTTTTGGAGCGGCACTACAGAAT Phytophthora_hibernalis TCCTGCCGTCTCGTGGTGAAGGATGGGGCCGGCCGCATGTCGAGGCTATGGCTATGGAGCGGCCTGTGATTGCTACTTTTTGGAGCGGCACTACGGAAT Phytophthora_ramorum_EU2 ACATGACGGAAGAAAACTCGTACCCGCTCAAGATTGACGGACTCATTGAGGTAAGCTTAAGCACACTGCCAGCAACTTTTGTGTGTGTGTGTGTGTG-- Phytophthora_ramorum_NA1a ACATGACGGAAGAAAACTCGTACCCGCTCAAGATTGACGGACTCATTGAGGTAAGCTTAAGCGCACTGCCAGCAACTTGTGTGTGTGTGTGTGTGTGTG Phytophthora_ramorum_NA1b ACATGACGGAAGAAAACTCGTACCCGCTCAAGATTGACGGACTCATTGAGGTAAGCTTAAGCGCACTGCCAGCAACTTGTGTGTGTGTGTGTGTGTG-- Phytophthora_ramorum_NA2a ACATGACGGAAGAAAACTCGTACCCGCTCAAGATTGACGGACTCATTGAGGTAAGCTTAAGCGCACTGCCAGCAACTTGTGTGTGTGTGTGTGTGTG-- Phytophthora_ramorum_NA2b ACATGACGGAAGAAAACTCGTACCCGCTCAAGATTGACGGACTCATTGAGGTAAGCTTAAGCGCACTGCCAGCAACTTGTGTGTGTGTGTGTGTGTG-- Phytophthora_ramorum_EU1a ACATGACGGAAGAAAACTCGTACCCGCTCAAGATTGACGGACTCATTGAGGTAAGCTTAAGCGCACTGCCAGCAACTTGTGTGTGTGTGTGTGTGTGTG Phytophthora_ramorum_EU1b ACATGACGGAAGAAAACTCGTACCCGCTCAAGATTGACGGACTCATTGAGGTAAGCTTAAGCACACTGCCAGCAACTTTTGTGTGTGTGTGTGTGCGTG Phytophthora_lateralis ACATGACGGAGCAAAACTCGTACCCGCTTAAGATTGACGGACTCATTGAGGTAAGCTGAAGCGCACTGCCAGCAAGTTTTGTATGTGTG-----G---- Phytophthora_hibernalis ATATGACGGAGGAAAACTCGTACCCGCTTAAGATTGACGGACTTGTTGAGGTAAGCT---GCACAC------CAGTTTTCTTAAATGGATTGGTG---- Phytophthora_ramorum_EU2 --------GCTGAGTGCCTTTGGATGTTCGTGTAGATTACAGAAGGAGCATTTCGAGGTCACATGTGGGCCGATCCCTCTGTGGAGCATCTGAAAGAGT Phytophthora_ramorum_NA1a TGTGTGTGGCTGAGTGCCTTTGGATGTTCGTGTAGATTACAGAAGGAGCATTTCGAGGTCACATGTGGGCCGATCCCTCTGTGGAGCATCTGAAAGAGT Phytophthora_ramorum_NA1b --------GCTGAGTGCCTTTGGATGTTCGTGTAGATTACAGAAGGAGCATTTCGAGGTCACATGTGGGCCGATCCCTCTGTGGAGCATCTGAAAGAGT Phytophthora_ramorum_NA2a --------GCTGAGTGCCTTTGGATGTTCGTGTAGATTACAGAAGGAGCATTTCGAGGTCACATGTGGGCCGATCCCTCTGTGGAGCATCTGAAAGAGT Phytophthora_ramorum_NA2b --------GCTGAGTGCCTTTGGATGTTCGTGTAGATTACAGAAGGAGCATTTCGAGGTCACATGTGGGCCGATCCCTCTGTGGAGCATCTGAAAGAGT Phytophthora_ramorum_EU1a TGTGTG--GCTGAGTGCCTTTGGATGTTCGTGTAGATTACAGAAGGAGCATTTCGAGGTCACATGTGGGCCGATCCCTCTGTGGAGCATCTGAAAGAGT Phytophthora_ramorum_EU1b --------GCTGAGTGCCTTTGGATGTTCGTGTAGATTACAGAAGGAGCATTTCGAGGTCACATGTGGGCCGATCCCTCTGTGGAGCATCTGAAAGAGT Phytophthora_lateralis ---------CTGAGTGTTTTTGGATGTTCGTGTAGATTACGGAAGGGGCCTTTCGAGGTCACATGTGGGCCGATCCCTCTGTGGAGCATCTGAAAGAGT Phytophthora_hibernalis --------GCTGAGTG--TCTGGATATTCGTGTAGATTCCGGAAGGAGCATTTCGAGGTCACATGTGGGCCGAGCCCTCTCTGGAGCATCTGAAAGAGT Phytophthora_ramorum_EU2 TGCTGCTTCGTGTGAAGGAGTTCCCTGAGGTACGGTGTATGAACTGTGATTCCTCTTTGCACTTTGAATTCTGACG-----CTAGGGCTTGTTGCTAAT Phytophthora_ramorum_NA1a TGCTGCTTCGTGTGAAGGAGTTCCCTGAGGTACGGTGTATGAACTGTGATTCCTCTTCGCACTTTGAATTCTGACG-----CTAGGGCTTGTTGCTAAT Phytophthora_ramorum_NA1b TGCTGCTTCGTGTGAAGGAGTTCCCTGAGGTACGGTGTATGAACTGTGATTCCTCTTTGCACTTTGAATTCTGACG-----CTAGGGCTTGTTGCTGAT Phytophthora_ramorum_NA2a TGCTGCTTCGTGTGAAGGAGTTCCCTGAGGTACGGTGTATGAACTGTGATTCCTCTTTGCACTTTGAATTCTGACG-----CTAGGGCTTGTTGCTGAT Phytophthora_ramorum_NA2b TGCTGCTTCGTGTGAAGGAGTTCCCTGAGGTACGGTGTATGAACTGTGATTCCTCTTTGCACTTTGAATTCTGACG-----CTAGGGCTTGTTGCTGAT Phytophthora_ramorum_EU1a TGCTGCTTCGTGTGAAGGAGTTCCCTGAGGTACGGTGTATGAACTGTGATTCCTCTTCGCACTTTGAATTCTGACG-----CTAGGGCTTGTTGCTAAT Phytophthora_ramorum_EU1b TGCTGCTTCGTGTGAAGGAGTTCCCTGAGGTACGGTGTATGAACTGTGATTCCTCTTTGCACTTTGAATTCTGACG-----CTAGGGCTTGTTGCTGAT Phytophthora_lateralis TGCTGCTTCGTGTGAAGGAGCATCCTGAGGTACGGCGTATGAACTGTGGTTCGTCTTTGCATCTTGAATTCTGACG-----CCAGGACTTGTTGTTGAT Phytophthora_hibernalis TGCTGCTTCGTGTGAAGGAGCATCCTGAGGTATGGCGTATGAAGTGTGATTCGTTTTTGCAGCTTGTAGTCTGACGATGTCTTGCTGTTAATTGTTAAT Phytophthora_ramorum_EU2 TGCAGGAAGCAGCGGGGAAAGGCAAGCAAGCGAGAGAAGACATGGTGGCCAAATACTCTCCAGAAATCGT Phytophthora_ramorum_NA1a TGCAGGAAGCAGCGGGGAAAGGCAAGCAAGCGAGAGAAGACATGGTGGCCAAATACTCTCCAGAAATCGT Phytophthora_ramorum_NA1b TGCAGGAAGCAGCGGGGAAAGGCAAGCAAGCGAGAGAAGACATGGTGGCCAAATACTCTCCAGAAATCGT Phytophthora_ramorum_NA2a TGCAGGAAGCAGCGGGGAAAGGCAAGCAAGCGAGAGAAGACATGGTGGCCAAATACTCTCCAGAAATCGT Phytophthora_ramorum_NA2b TGCAGGAAGCAGCGGGGAAAGGCAAGCAAGCGAGAGAAGACATGGTGGCCAAATACTCTCCAGAAATCGT Phytophthora_ramorum_EU1a TGCAGGAAGCAGCGGGGAAAGGCAAGCAAGCGAGAGAAGACATGGTGGCCAAATACTCTCCAGAAATCGT Phytophthora_ramorum_EU1b TGCAGGAAGCAGCGGGGAAAGGCAAGCAAGCGAGAGAAGACATGGTGGCCAAATACTCTCCAGAAATCGT Phytophthora_lateralis TGCAGGAAGCAGCAGCGAAAGGCAAGCGAGCGAGAGAAGACATGGTGGCTAAATACTCTCCAGAAATCGT Phytophthora_hibernalis CGCAGGAAGCAGCGGCGAAAGGCAAGCGAGCGAGGGAAGACATGGTCGCCAAATACTCCCCAGAAATCGT ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 664; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 664; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 664; END; BEGIN TREES; Title tree_gwEuk; LINK Taxa = Taxa; TRANSLATE 1 Phytophthora_ramorum_EU2, 2 Phytophthora_ramorum_NA1a, 3 Phytophthora_ramorum_NA1b, 4 Phytophthora_ramorum_NA2a, 5 Phytophthora_ramorum_NA2b, 6 Phytophthora_ramorum_EU1a, 7 Phytophthora_ramorum_EU1b, 8 Phytophthora_lateralis, 9 Phytophthora_hibernalis; TREE Imported_tree_0 = ((((((2:0.0,6:0.0)0.9330:0.00158739,1:0.00319116)0.6010:0.00318551,(3:0.0,4:0.0):2.92E-6)0.6880:0.00638352,5:2.63E-6)0.5590:0.00357821,7:0.00440014)1.0000:0.03459075,8:0.03710672,9:0.09237104); END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1345816224129; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 3255606621922177776; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 294712731799949242; mqVersion 275; checksumv 0 3 3278410660 null getNumChars 664 numChars 664 getNumTaxa 9 numTaxa 9 short true bits 15 states 15 sumSquaresStatesOnly 126820.0 sumSquares 126820.0 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 1867 541; setLocation 91 42; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #3255606621922177776 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 9164.1345816163777.2989062574040867998; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1767 474; setLocation 91 42; 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 '(((((((2:0.0,6:0.0)0.9330:0.00158739,1:0.00319116)0.6010:0.00318551,(3:0.0,4:0.0):2.92E-6)0.6880:0.00638352,5:2.63E-6)0.5590:0.00357821,7:0.00440014)1.0000:0.03459075,8:0.03710672):0.04618552,9:0.04618552)<> <> < 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; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #294712731799949242 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 163; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1767 474; setLocation 91 42; 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;