#NEXUS [written Fri Aug 24 15:16:38 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_EU2a Phytophthora_ramorum_EU2b Phytophthora_ramorum_NA1 Phytophthora_ramorum_EU1a Phytophthora_ramorum_EU1b Phytophthora_ramorum_NA2a Phytophthora_ramorum_NA2b Phytophthora_hibernalis Phytophthora_lateralis ; END; BEGIN CHARACTERS; TITLE alignment_Avh120; DIMENSIONS NCHAR=387; FORMAT DATATYPE = DNA INTERLEAVE GAP = - MISSING = ?; MATRIX Phytophthora_ramorum_EU2a ATGCGCCTGAGTCTCTTCCTGCTGCTTGTGGTCCTCGCCTTCGTCGCATGCTGTAGCACCGTCGTGGCTGCTGAAGAAGCTGTCCAAGCTAGCAACCTG Phytophthora_ramorum_EU2b ATGCGCCTGAGTCTCTTCCTGCTGCTTGTGGTCCTCGCCTTCGTCGCATGCTGTAGCACCGTCGTGGCTACTGAAGAAGCTGTCCAAGCCAGCAACCTG Phytophthora_ramorum_NA1 ATGCGCCTGAGTCTCTTCCTGCTGCTTGTGGTCCTCGCCTTCGTCGCATGCTGTAGCACCGTCGTGGCTACTGAAGAAGCTGTCCAAGCCAGCAACCTG Phytophthora_ramorum_EU1a ATGCGCCTGAGTCTCTTCCTGCTGCTTGTGGTCCTCGCCTTCGTCGCATGCTGTAACACCGTCGTGGCTGCTGAAGAAGCTGTCCAAGCCAGCAACCTG Phytophthora_ramorum_EU1b ATGCGCCTGAGTCTCTTCCTGCTGCTTGTGGTCCTCGCCTTCGTCGCATGCTGTAACACCGTCGTGGCTGCTGAAGAAGCTGTCCAAGCCAGCAACCTG Phytophthora_ramorum_NA2a ATGCGCCTGAGTCTCTTCCTGCTGCTTGTGGTCCTCGCCTTCGTCGCATGCTGTAACACCGTCGTGGCTGCTGAAGAAGCTGTCCAAGCTAGCAACCTG Phytophthora_ramorum_NA2b ATGCGCCTGAGTCTCTTCCTGCTGCTTGTGGTCCTCGCCTTCGTCGCATGCTGTAGCACCGTCTTGGCTGCTGAAGAAGCTGTCCAAGCCAGCAACCTG Phytophthora_hibernalis ATGCATCGAAGCCTCTTCCTACTGGTTGTGATCCTCGCCTTCGTAGCACACTGCAGGACCATCGTGGCTGCCGAAGAAGCTGTCCAGATCAGCAACCTG Phytophthora_lateralis ATGCGCCTGAGTCTCTTCCTACTGCTTGTGATTCTCGCCTTTGTCGCATGCTGTAGCACCATCGTGGCTGCTGATGAAGCTGTCCAGACTAGCAACCTG Phytophthora_ramorum_EU2a GTCCCCGAGTCCAACCAAAATCTTGCCGGCGAAAGCCACCGCAACCTGAAGGGAAGCAAAACGACTACCACTGCTGACGCGGAGAGTGAAGAGCGAGTT Phytophthora_ramorum_EU2b GTCCCCGAGTCCAACCAAAATCTTGCCGGCGAAAGCCACCGCAACCTGAAGGGAAGCAAAACGACTACCACTGCTGACGCGGAGAGTGAAGAGCGAGTT Phytophthora_ramorum_NA1 GTCCCCGAGTCCAACCAAAATCTTGCCGGCGAAAGCCACCGCAACCTGAAGGGAAGCAAAACGACTACCACTGCTGACGCGGAGAGTGAAGAGCGAGTT Phytophthora_ramorum_EU1a GTCCCCGAGTCCAACCAATATCTTGCCGGCGAAAGCCACCGCAACCTGAAGGGAAGCAAAACAACTACCACTGCTGACGCGGAGAGTGAAGAGCGAGTT Phytophthora_ramorum_EU1b GTCCCCGAGTCCAACCAATATCTTGCCGGCGAAAGCCACCGCAACCTGAAGGGAAGCAAAACGACTACCACTGCTGACGCGGAGAGTGAAGAGCGAGTT Phytophthora_ramorum_NA2a GTCCCCGAGTCCAACCAAAATCTTGCCGGCGAAAGCCACCGCAACCTGAAGGGAAGCAAAACGACTACCACTGCTGACGCGGAGAGTGAAGAGCGAGTT Phytophthora_ramorum_NA2b GTCCCCGAGTCCAACCAAAATCTTGCCGGCGAAAGCCACCGCAACCTGAAGGGAAGCAAAACGACTACCACTGCTGACGCGGAGAGTGAAGAGCGAGTT Phytophthora_hibernalis ATGACTGACTCCGACCAAAACCTTGGCACTGAAGCCCACCGCAACCTGAAGGGAAGCAAAACGACTAACACAGCTGTTGTGGATAGCGAAGAGCGAGTT Phytophthora_lateralis GTTCCCGACTCCAA---AAATCTTGCCAGTGAAAGCCACCGCAACCTGAAGGGAAGCAAAACGACTACCACTACTGGCACGGAGCGTGAAGAGCGAGTT Phytophthora_ramorum_EU2a GGTGCCACAACCCCCAATTTCGGCATGCTCCAGGGGTTTCTCAGGCTCCCCAAGCTCCAAGGCCTCGCAAAACTTCCTTTGATTAAGCAGCTCACTCAG Phytophthora_ramorum_EU2b GGTGCCACAACCCCCAATTTCGGCATGCTCCAGGGGTTTCTCAGGCTCCCCAAGCTCCAAGGCCTCGCAAAACTTCCTTTGATTAAGCAGCTCACTCAG Phytophthora_ramorum_NA1 GGTGCCACAACCCCCAATTTCGGCATGCTCCAGGGGTTTCTCAAGCTCCCCAAGCTCCAAGGCCTCGCAAAACTTCCTTTGATTAAGCAGCTCACTCAG Phytophthora_ramorum_EU1a GGTGCCACAACCCCCAATTTCGGCATGCTCCAGGGGTTTCTCAAGCTCCCCAAGCTCCAAGGCCTCGCAAAACTTCCTTTGATTAAGCAGCTCACTCAG Phytophthora_ramorum_EU1b GGTGCCACAACCCCCAATTTCGGCATGCTCCAGGGGTTTCTCAAGCTCCCCAAGCTCCAAGGCCTCGCAAAACTTCCTTTGATTAAGCAGCTCACTCAG Phytophthora_ramorum_NA2a GGTGCCACAACCCCCAATTTCGGCATGCTCCAGGGGTTTCTCAAGCTCCCCAAGCTCCAAGGCCTCGCAAAACTTCCTTTGATTAAGCAGCTCACTCAG Phytophthora_ramorum_NA2b GGTGCCACAACCCCCAATTTCGGCATGCTCCAGGGGTTTCTCAAGCTCCCCAAGCTCCAAGGCCTCGCAAAACTTCCTTTGATTAAGCAGCTCACTCAG Phytophthora_hibernalis GGTTCCTCAGTCCCTAACTTCGGCATGCTTTCTGGATTGTTGAAGCTCCCCAAGCTCCAAGGCCTCGCAAAGCTCCCTTTGATTAAGCAGCTCCGTCAG Phytophthora_lateralis GGTGCCACAACCCCCAATTTCGGCATGCTCTGGGGGCTTCTCAGGCTCCCCAAGCTCCAAGGCCTCGCAAGACTTCCATTGATTAAGCAGCTCACTCAG Phytophthora_ramorum_EU2a ATCAGCCAAAAGTTTGGCAAGTACTCCAGCATCGTATTCCAGTGGCTCGTGAAAAAATTCCGTATCCACAACACCAATGCAAACATTTAG Phytophthora_ramorum_EU2b ATCAGCCAAAAGTTTGGCAAGTACTCCAGCAACGTATTCCAATGGCTCGTGAAAAAATTCCGTATCCACAACACCAATGCAAACATTTAG Phytophthora_ramorum_NA1 ATCAGCCAAAAGTTTGGCAAGTACTCCAGCAACGTATTCCAATGGCTCATGAAAAAATTCCGTATCTACAACACCAATGCAAACATTTAG Phytophthora_ramorum_EU1a ATCAGCCAAAAGTTTGGCAAGTACTCCAGCAACGTATTCCAATGGCTCATGAAAAAATTCCGTATCTACAACACCAATGCAAACATTTAG Phytophthora_ramorum_EU1b ATCAGCCAAAAGTTTGGCAAGTACTCCAGCAACGTATTCCAATGGCTCATGAAAAAATTCCGTATCTACAACACCAATGCAAACATTTAG Phytophthora_ramorum_NA2a ATCAGCCAAAAGTTTGGCAAGTACTCCAGCAACGTACTCCAATGGCTCATGAAAAAATTCCGTATCTACAACACCAATGCAAACATTTAG Phytophthora_ramorum_NA2b ATCAGCCAAAAGTTTGGCAAGTACTCCAGCAACGTATTCCAATGGCTCATGAAAAAATTCCGTATCTACAACACCAATGCAAACATTTAG Phytophthora_hibernalis ATCAGCCAAAAGTTTGGCAAGCACTCTGGCACCGCATTCCAATGGCTCATGAAAAAGCTCCATGGCAACAGCGTCAATGCAAACATTTAG Phytophthora_lateralis ATCAGCCAAAAGTTCGGCAAGTACGCTGGCGCCGTATTCCAATGGCTCGTGAGAAAGTTCCGTGACTACAACAACAATGCAAACATGTAA ; END; BEGIN TREES; Title tree_Avh120; LINK Taxa = Taxa; TRANSLATE 1 Phytophthora_ramorum_EU2a, 2 Phytophthora_ramorum_EU2b, 3 Phytophthora_ramorum_NA1, 4 Phytophthora_ramorum_EU1a, 5 Phytophthora_ramorum_EU1b, 6 Phytophthora_ramorum_NA2a, 7 Phytophthora_ramorum_NA2b, 8 Phytophthora_hibernalis, 9 Phytophthora_lateralis; TREE Imported_tree_0 = (((((((4:0.00260811,5:0.0)0.8250:0.00262562,6:0.00523107)0.6000:0.00260616,7:0.00262166)0.5020:0.00260908,3:3.8E-7)0.5990:0.00784814,2:0.0)0.5500:0.00759262,1:0.00303781)0.9570:0.04539311,9:0.05328611,8:0.18384393); END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 387; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 387; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 387; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1345814198971; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 7916695232616633950; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 6282413496599252997; mqVersion 275; checksumv 0 3 1292986387 null getNumChars 387 numChars 387 getNumTaxa 9 numTaxa 9 short true bits 15 states 15 sumSquaresStatesOnly 64677.0 sumSquares 64677.0 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 1458 623; setLocation 37 20; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #7916695232616633950 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 4442.1345799517303.3082804111800451944; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1358 556; setLocation 37 20; 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 '((((((((4:0.00260811,5:0.0)0.8250:0.00262562,6:0.00523107)0.6000:0.00260616,7:0.00262166)0.5020:0.00260908,3:3.8E-7)0.5990:0.00784814,2:0.0)0.5500:0.00759262,1:0.00303781)0.9570:0.04539311,9:0.05328611):0.091921965,8:0.091921965);'; 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;