#NEXUS [written Mon Oct 03 11:23:45 ICT 2011 by Mesquite version 2.74 (build 550) at iman/172.20.20.118] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=8; TAXLABELS Sawadaea_nankinensis C._lanestris_ex_Myrica_californica_AF011288_USA C._lanestris_ex_Quercus_agrifolia_AB000933_USA C._lanestris_ex_Quercus_agrifolia_AF011289_USA C._lanestris_ex_Quercus_sp._AF073354_KOR C._wrightii_ex_Quercus_glauca_AB000932_JPN C._tjibodensis_ex_Castanopsis_argentea_T C._tjibodensis_ex_Castanopsis_argentea_A ; END; BEGIN CHARACTERS; TITLE 'Matrix in file "Cystotheca_tjibodensis.nexus"'; DIMENSIONS NCHAR=488; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Sawadaea_nankinensis CTGAGCGTGA-GCCACGCAGGGCGC---AAGCCCCGCGCGGCCGACCCTCCACCCGTGCCGACTCATATCCGGTTGCCCTGGCGG--------------CCTGCCGGCCCCGGCTGGCA-GTGCCCGCGAGAGGCGCCCCAACTCGTGCTGTCAGTGATGTCTGAGTCGCAGTTAA--TAAAGTAAAACTTTCAACAACGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTTAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCCCGGTATTCCGAGGGGCATGCCTGTTCGAGCGTCATAACAACCCCTCAAGCCTAGCTTGGTCTTGGGGCCCG-CCGGCCTGGCGGCCCTTAAACACAGTGGCGGCGCCGCCGCGCTCTACGCGTAGTAACTCTTCTCGCGACAGGGCGCAGGCGGGGCCAGCCGAAGCACCCCCTTCTCTCGG C._lanestris_ex_Myrica_californica_AF011288_USA ---------------CGCTGGGCGCCTGGCGCCGGGCGTGGCTGACCCTCCACCCGTGTCTA-TCTTCTCATGTTGCTTTGGCGGGCCGGGCCGCGTGCCCTCCTGGCACCTGCTGGGACGTGCCCGCCAGAGCCCCCTTAACGCGTGCTGTTTGTGTGGTCAGAGTGGTAGCAAAATTAGAATAAAACTTTCAACAACGGATCTCTTGGCTCCGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTTAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCCCGGTATTCCGAGGGGCATGCCTGTCCGAGCGTCAGTACAACCCCTCAAGCCTAGCTTGGTCTTGGGGCGCGCCCTGAGGGGCAGCCCTTAAATGCAGTGGCGGTGCCGTCCGGCTCTACGCGTAGTTATTTCTCTCGCGACAGGGTGGTGACGGGACCTGCCAGAATACCCATCTTAACAGG C._lanestris_ex_Quercus_agrifolia_AB000933_USA CTGAGCGTGAGGCCACGCTGGGCGCCTGGCGCCGGGCGTGGCTGACCCTCCACCCGTGTCTA-TCTTCTCATGTTGCTTTGGCGGGCCGGGCCGCGTGCCCTCCTGGCACCTGCTGGGACGTGCCCGCCAGAGCCCCCTTAACGCGTGCTGTTTGTGTGGTCAGAGTGGTAGCAAAATTAGAATAAAACTTTCAACAACGGATCTCTTGGCTCCGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTTAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCCCGGTATTCCGAGGGGCATGCCTGTCCGAGCGTCAGTACAACCCCTCAAGCCTAGCTTGGTCTTGGGGCGCGCCCTGAGGGGCAGCCCTTAAATGCAGTGGCGGTGCCGTCCGGCTCTACGCGTAGTTATTTCTCTCGCGACAGAGTGGTGACGGGACCTGCCAGAATACCCATCTTAACAGG C._lanestris_ex_Quercus_agrifolia_AF011289_USA ------------GCACGCTGGGCGCCTGGCGCCGGGCGTGGCTGACCCTCCACCCGTGTCTA-TCTTCTCATGTTGCTTTGGCGGGCCGGGCCGCGTGCCCTCCTGGCACCTGCTGGGACGTGCCCGCCAGAGCCCCCTTAACGCGTGCTGTTTGTGTGGTCAGAGTGGTAGCAAAATTAGAATAAAACTTTCAACAACGGATCTCTTGGCTCCGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTTAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCCCGGTATTCCGAGGGGCATGCCTGTCCGAGCGTCAGTACAACCCCTCAAGCCTAGCTTGGTCTTGGGGCGCGCCCTGAGGGGCAGCCCTTAAATGCAGTGGCGGTGCCGTCCGGCTCTACGCGTAGTTATTTCTCTCGCGACAGGGTGGTGACGGGACCTGCCAGAATACCCATCTTAACAGG C._lanestris_ex_Quercus_sp._AF073354_KOR CTGAGCGTGAAGCCACGCTGGGCGCCTGGCGCCGGGCGTGGCTGACCCTCCACCCGTGTCTA-TCTTCTCATGTTGCTTTGGCGGGCCGGGCCTTGCGCCCTCCTGGCACCTGCTGGGACGTGCCCGCCAGAGCCCCCTTAACGCGTGCTGTTTGTGTGGTCAGAGTGGTAGCAGAATTAGAATAAAACTTTCAACAACGGATCTCTTGGCTCCGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTTAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCCCGGTATTCCGAGGGGCATGCCTGTCCGAGCGTCAGTACAACCCCTCAAGCCTAGCTTGGTCTTGGGGCGCGCCCTATGGGGCAGCCCTTAAATGCAGTGGCGGTGCCGTCCGGCTCTACGCGTAGTTATTTCTCTCGCGACAGAGTGGTGACGGGACCTGCCAGAACACCCATTCTAACAGG C._wrightii_ex_Quercus_glauca_AB000932_JPN CTGAGCGTGAGGCCACGCTGGGCGCCTGGCGCCAGGCGTGGCTGACCCTCCACCCGTGTCTA-TCTTCTCATGTTGCTTTGGCGGGCCGGGCCCTGTGCCCTCCCGGCGCCTGCTGGGACGCGCCCGCCAGAGCCACCCTAACGCGTGCTGTTTGTGTGGTCAGAGTGGTAGCAGAATTAGAATAAAACTTTCAACAACGGATCTCTTGGCTCCGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTTAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCCCGGTATTCCGAGGGGCATGCCTGTCCGAGCGTCAGTACAACCCCTCAAGCCTGGCTTGGTCTTGGAGCGCGCCCCGCGGGGCGGCTCTTAAATGCAGTGGCGGTGCCGTCGGGCTCTACGCGTAGTTATTTCTCTCGCGACAGGGTGGTGACGGGACCTGCCAGAAGCCTCATCATACTAGG C._tjibodensis_ex_Castanopsis_argentea_T ---GACGTGAGGCCACGCTGGGCGCCTGGCGCCTGGCGGGGCTGACCCTCCACCCGTGTCTA-TCTTCTCATGTTGCTTTGGCGGGCCGGGCCTCGTGCCCTCCCGGCGTCGGCTGGGACGCGCCCGCCAGAGCCCCCCTAACGCGTGCTGTTTGTGTGGTCAGAGTGGTAGCAGAATTAGAATAAAACTTTCAACAACGGATCTCTTGGCTCCGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTTAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCCCGGTATTCCGAGGGGCATGCCTGTCCGAGCGTCAGTACAACCCCTCAAGCGTAGCTTGGTCTTGGGGCGCGCCCCGCGGGGCGGCCCTTAAATGCAGTGGCGGTGCCGTTGGGCTCTACGCGTAGTTATTTCTCTCGCG------------------------------------------- C._tjibodensis_ex_Castanopsis_argentea_A -------------------------------------------------CCACCCGTGTCTA-TCTTCTCATGTTGCTTTGGCGGGCCGGGCCTCGTGCCCTCCCGGCGTCGGCTGGGACGCGCCCGCCAGAGCCCCCCTAACGCGTGCTGTTTGTGTGGTCAGAGTGGTAGCAGAATTAGAATAAAACTTTCAACAACGGATCTCTTGGCTCCGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTTAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCCCGGTATTCCGAGGGGCATGCCTGTCCGAGCGTCAGTACAACCCCTCAAGCGTAGCTTGGTCTTGGGGCGCGCCCCGCGGGGCGGCCCTTAAATGCAGTGGCGGTGCCGTTGGGCTCTACGCGTAGTTATTTCTCTCGCGACAGGGTGGTGACGGGACTTGCCAAAAGGCTCATCTCATTCGG ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 488; END; BEGIN TREES; Title 'Trees from "Best2.tre"'; LINK Taxa = Taxa; TRANSLATE 1 Sawadaea_nankinensis, 2 C._lanestris_ex_Myrica_californica_AF011288_USA, 3 C._lanestris_ex_Quercus_agrifolia_AB000933_USA, 4 C._lanestris_ex_Quercus_agrifolia_AF011289_USA, 5 C._lanestris_ex_Quercus_sp._AF073354_KOR, 6 C._wrightii_ex_Quercus_glauca_AB000932_JPN, 7 C._tjibodensis_ex_Castanopsis_argentea_T, 8 C._tjibodensis_ex_Castanopsis_argentea_A; TREE PAUP_1 = (1,(((((2,4),3),5),6),(7,8))); TREE PAUP_2 = (1,((((2,3,4),5),6),(7,8))); END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 488; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 488; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1317615825406; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 3012933125706565942; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 3804857011208146263; mqVersion 274; checksumv 0 2 1546405606 null getNumChars 488 numChars 488 getNumTaxa 8 numTaxa 8 short true bits 15 states 15 sumSquaresStatesOnly 75870.0 sumSquares 75870.0 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 1366 622; setLocation -4 -4; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #3012933125706565942 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #3012933125706565942; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1266 555; setLocation -4 -4; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; endTell; showWindow; getEmployee #mesquite.lists.ColorTaxon.ColorTaxon; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #3012933125706565942 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 870.1317615789140.7450675694033937257; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1266 555; setLocation -4 -4; setFont SanSerif; setFontSize 10; getToolPalette; tell It; 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 off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; 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; 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; 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 #3804857011208146263 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1266 555; setLocation -4 -4; 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; showWindow; getWindow; tell It; forceAutosize; endTell; 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;