#NEXUS [written Wed Mar 28 14:54:49 CEST 2012 by Mesquite version 2.75 (build 564) at romon-9b2ca854d/127.0.0.1] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=25; TAXLABELS O_euskadiensis_CMW27318_SPAIN O_euskadiensis_CMW27898_SPAIN O_euskadiensis_CMW27899_SPAIN O_cf_abietinum_EU785433_CHINA O_cf_abietinum_EU785434_CHINA O_cf_abietinum_AY280470_USA O_cf_abietinum_AY280469_USA O_cf_abietinum_CMW397_SA O_cf_abietinum_AY280468_CANADA O_cf_abietinum_DQ865287_CANADA Sporothrix_sp_1_CMW9488_MEXICO Sporothrix_sp_1_CMW9491_MEXICO O_abietinum_HM067820_T Sporothrix_sp_2_CMW9487_MEXICO Sporothrix_sp_2_CMW9489_MEXICO O_fusiforme_AY280464_AUSTRIA O_fusiforme_AY280465_AUSTRIA O_lunatum_AY280466_AUSTRIA O_lunatum_AY280467_AUSTRIA O_fusiforme_AY280462_AZERBAIJAN O_fusiforme_AY280461_AZERBAIJAN O_fusiforme_AY280463_AZERBAIJAN O_cf_abietinum_HM031568_RUSSIA Ophiostoma_stenoceras_DQ296074_T O_stenoceras ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=242; FORMAT DATATYPE = DNA INTERLEAVE GAP = - MISSING = -; MATRIX O_euskadiensis_CMW27318_SPAIN ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtccagcccactcagtttgaaaacgatgt----gaacagct O_euskadiensis_CMW27898_SPAIN ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtccagcccactcagtttgaaaacgatgt----gaacagct O_euskadiensis_CMW27899_SPAIN ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtccagcccactcagtttgaaaacgatgt----gaacagct O_cf_abietinum_EU785433_CHINA ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtccagcccaccccgtgtgaaaacgatgt----gaacagct O_cf_abietinum_EU785434_CHINA ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtccagcccaccccgtgtgaaaacgatgt----gaacagct O_cf_abietinum_AY280470_USA ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtccagcccacccagtgtgaaaacgatgt----gaacagct O_cf_abietinum_AY280469_USA ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtccagcccacccagtgtgaaaacgatgt----gaacagct O_cf_abietinum_CMW397_SA ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtccagcccacccagtgtgaaaacgatgt----gaacagct O_cf_abietinum_AY280468_CANADA ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtccagcccacccagtgtgaaaacgatgt----gaacagct O_cf_abietinum_DQ865287_CANADA ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtccagcccacccagtgtgaaaacgatgt----gaacagct Sporothrix_sp_1_CMW9488_MEXICO ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtctagcccacccagtgtgaaaacgatgt----gaacagct Sporothrix_sp_1_CMW9491_MEXICO ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtctagcccacccagtgtgaaaacgatgt----gaacagct O_abietinum_HM067820_T ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtccagcccacccaatgtgaaaacgatgt----gaatagct Sporothrix_sp_2_CMW9487_MEXICO ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtccagcccacccagtgtgaaaacgatgt----gaacagct Sporothrix_sp_2_CMW9489_MEXICO ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtccagcccacccagtgtgaaaacgatgt----gaacagct O_fusiforme_AY280464_AUSTRIA ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtccagcccacccagtgtgaaaacgatat----gaacagct O_fusiforme_AY280465_AUSTRIA ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtccagcccacccagtgtgaaaacgatat----gaacagct O_lunatum_AY280466_AUSTRIA ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtccagcccacccagtgtgaaaacgatat----gaacagct O_lunatum_AY280467_AUSTRIA ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtccagcccacccagtgtgaaaacgatat----gaacagct O_fusiforme_AY280462_AZERBAIJAN ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtccagcccacccagtgtgaaaacgatat----gaacagct O_fusiforme_AY280461_AZERBAIJAN ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtccagcccacccagtgtgaaaacgatat----gaacagct O_fusiforme_AY280463_AZERBAIJAN ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtccagcccacccagtgtgaaaacgatat----gaacagct O_cf_abietinum_HM031568_RUSSIA ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagttctgcccacccagtgtgaaaacgatat----gaacagct Ophiostoma_stenoceras_DQ296074_T ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtactaacgcctccatgactatattatattctaggagagtg O_stenoceras ctacaacggcacctcggacctccagctggagcgtctgagcgtctacttcaacgaggtcagtactaacgcctccatgactatattatattctaggagagtg O_euskadiensis_CMW27318_SPAIN tcctaacattgtgcattgtgtaggcctccggcaacaagtacgtcccccgtgccgtccttgtcgatcttgagcccggtaccatggacgccgtccgcgctgg O_euskadiensis_CMW27898_SPAIN tcctaacattgtgcattgtgtaggcctccggcaacaagtacgtcccccgtgccgtccttgtcgatcttgagcccggtaccatggacgccgtccgcgctgg O_euskadiensis_CMW27899_SPAIN tcctaacattgtgcattgtgtaggcctccggcaacaagtacgtcccccgtgccgtccttgtcgatcttgagcccggtaccatggacgccgtccgcgctgg O_cf_abietinum_EU785433_CHINA tcctaa-------cgttgtgtaggcctccggcaacaagtacgtcccccgtgccgtccttgtcgatcttgagcccggtaccatggacgccgtccgcgctgg O_cf_abietinum_EU785434_CHINA tcctaa-------cgttgtgtaggcctccggcaacaagtacgtcccccgtgccgtccttgtcgatcttgagcccggtaccatggacgccgtccgcgctgg O_cf_abietinum_AY280470_USA tcctaa-------cattgtgtaggcctccggcaacaagtacgtcccccgtgccgtccttgtcgatcttgaacccggtaccatggacgccgtccgcgctgg O_cf_abietinum_AY280469_USA tcctaa-------cattgtgtaggcctccggcaacaagtacgtcccccgtgccgtccttgtcgatcttgaacccggtaccatggacgccgtccgcgctgg O_cf_abietinum_CMW397_SA tcctaa-------cattgtgtaggcctccggcaacaagtacgtcccccgtgccgtccttgtcgatcttgaacccggtaccatggacgccgtccgcgctgg O_cf_abietinum_AY280468_CANADA tcctaa-------cattgtgtaggcctccggcaacaagtacgtcccccgtgccgtccttgtcgatcttgagcccggtaccatggacgccgtccgcgctgg O_cf_abietinum_DQ865287_CANADA tcctaa-------cattgtgtaggcctccggcaacaagtacgtcccccgtgccgtccttgtcgatcttgagcccggtaccatggacgccgtccgcgctgg Sporothrix_sp_1_CMW9488_MEXICO tcctaa-------cattgtgtaggcctccggcaacaagtacgtcccccgtgccgtccttgtcgatcttgagcccggtaccatggacgccgtccgcgctgg Sporothrix_sp_1_CMW9491_MEXICO tcctaa-------cattgtgtaggcctccggcaacaagtacgtcccccgtgccgtccttgtcgatcttgagcccggtaccatggacgccgtccgcgctgg O_abietinum_HM067820_T tcctaa-------cattgtgtaggcctccggcaacaagtacgtcccccgtgccgtccttgtcgatcttgagcccggtaccatggacgccgtccgcgctgg Sporothrix_sp_2_CMW9487_MEXICO tcctaacattgtgcattgtgtaggcctccggcaacaagtacgtcccccgtgccgtccttgtcgatcttgagcccggtaccatggacgccgtccgcgctgg Sporothrix_sp_2_CMW9489_MEXICO tcctaacattgtgcattgtgtaggcctccggcaacaagtacgtcccccgtgccgtccttgtcgatcttgagcccggtaccatggacgccgtccgcgctgg O_fusiforme_AY280464_AUSTRIA tcctaa-------cattgtgtaggcctccggcaacaagtacgtcccccgtgccgtccttgtcgatcttgagcccggtaccatggacgccgtccgcgctgg O_fusiforme_AY280465_AUSTRIA tcctaa-------cattgtgtaggcctccggcaacaagtacgtcccccgtgccgtccttgtcgatcttgagcccggtaccatggacgccgtccgcgctgg O_lunatum_AY280466_AUSTRIA tcctaa-------cattgtgtaggcctccggcaacaagtacgtcccccgtgccgtccttgtcgatcttgagcccggtaccatggacgccgtccgcgctgg O_lunatum_AY280467_AUSTRIA tcctaa-------cattgtgtaggcctccggcaacaagtacgtcccccgtgccgtccttgtcgatcttgagcccggtaccatggacgccgtccgcgctgg O_fusiforme_AY280462_AZERBAIJAN tcctaa-------cattgtgtaggcctccggcaacaagtacgtcccccgtgcggtccttgtcgatcttgagcccggtaccatggacgccgtccgcgctgg O_fusiforme_AY280461_AZERBAIJAN tcctaa-------cattgtgtaggcctccggcaacaagtacgtcccccgtgcggtccttgtcgatcttgagcccggtaccatggacgccgtccgcgctgg O_fusiforme_AY280463_AZERBAIJAN tcctaa-------cattgtgtaggcctccggcaacaagtacgtcccccgtgcggtccttgtcgatcttgagcccggtaccatggacgccgtccgcgctgg O_cf_abietinum_HM031568_RUSSIA tcctaa-------cattgtgtaggcctccggcaacaagtacgtcccccgtgccgtcctcgtcgatcttgagcccggtaccatggacgccgtccgcgctgg Ophiostoma_stenoceras_DQ296074_T acacta-------acaactgtaggcctccggtaacaagtacgtcccccgtgccgtccttgtcgatctggagcccggcaccatggacgccgtccgtgctgg O_stenoceras acacta-------acaactgtaggcctccggtaacaagtacgtcccccgtgccgtccttgtcgatctggagcccggcaccatggacgccgtccgtgctgg O_euskadiensis_CMW27318_SPAIN tcctttcggccagctgttccgccccgacaacttcgtc-tcgg O_euskadiensis_CMW27898_SPAIN tcctttcggccagctgttccgccccgacaacttcgtc-tcgg O_euskadiensis_CMW27899_SPAIN tcctttcggccagctgttccgccccgacaacttcgtc-tcgg O_cf_abietinum_EU785433_CHINA tcctttcggccagctgttccgccccgacaacttcgtcttcgg O_cf_abietinum_EU785434_CHINA tcctttcggccagctgttccgccccgacaacttcgtcttcgg O_cf_abietinum_AY280470_USA tcctttcggccagctgttccgccccgacaacttcgtcttcgg O_cf_abietinum_AY280469_USA tcctttcggccagctgttccgccccgacaacttcgtcttcgg O_cf_abietinum_CMW397_SA tcctttcggccagctgttccgccccgacaacttcgtcttcgg O_cf_abietinum_AY280468_CANADA tcctttcggccagctgttccgccccgacaacttcgtcttcgg O_cf_abietinum_DQ865287_CANADA tcctttcggccagctgttccgccccgacaacttcgtcttcgg Sporothrix_sp_1_CMW9488_MEXICO tcctttcggccagctgttccgccccgacaacttcgtcttcgg Sporothrix_sp_1_CMW9491_MEXICO tcctttcggccagctgttccgccccgacaacttcgtcttcgg O_abietinum_HM067820_T tcctttcggccagctgttccgccccgacaacttcgtcttcgg Sporothrix_sp_2_CMW9487_MEXICO tcctttcggccagctgttccgccccgacaacttcgtcttcgg Sporothrix_sp_2_CMW9489_MEXICO tcctttcggccagctgttccgccccgacaacttcgtcttcgg O_fusiforme_AY280464_AUSTRIA tcctttcggccagctgttccgccccgacaactttgtcttcgg O_fusiforme_AY280465_AUSTRIA tcctttcggccagctgttccgccccgacaactttgtcttcgg O_lunatum_AY280466_AUSTRIA tcctttcggccagctgttccgccccgacaactttgtcttcgg O_lunatum_AY280467_AUSTRIA tcctttcggccagctgttccgccccgacaactttgtcttcgg O_fusiforme_AY280462_AZERBAIJAN tcctttcggccagctgttccgccccgacaactttgtcttcgg O_fusiforme_AY280461_AZERBAIJAN tcctttcggccagctgttccgccccgacaactttgtcttcgg O_fusiforme_AY280463_AZERBAIJAN tcctttcggccagctgttccgccccgacaactttgtcttcgg O_cf_abietinum_HM031568_RUSSIA tcctttcggccagctgttccgccccgacaacttcgtcttcgg Ophiostoma_stenoceras_DQ296074_T tcctttcggccagctgttccgccccgacaatttcgtcttcgg O_stenoceras tcctttcggccagctgttccgccccgacaatttcgtcttcgg ; END; BEGIN TREES; Title 'Trees from "bttree.tre"'; LINK Taxa = Taxa; TRANSLATE 1 O_euskadiensis_CMW27318_SPAIN, 2 O_euskadiensis_CMW27898_SPAIN, 3 O_euskadiensis_CMW27899_SPAIN, 4 O_cf_abietinum_EU785433_CHINA, 5 O_cf_abietinum_EU785434_CHINA, 6 O_cf_abietinum_AY280470_USA, 7 O_cf_abietinum_AY280469_USA, 8 O_cf_abietinum_CMW397_SA, 9 O_cf_abietinum_AY280468_CANADA, 10 O_cf_abietinum_DQ865287_CANADA, 11 Sporothrix_sp_1_CMW9488_MEXICO, 12 Sporothrix_sp_1_CMW9491_MEXICO, 13 O_abietinum_HM067820_T, 14 Sporothrix_sp_2_CMW9487_MEXICO, 15 Sporothrix_sp_2_CMW9489_MEXICO, 16 O_fusiforme_AY280464_AUSTRIA, 17 O_fusiforme_AY280465_AUSTRIA, 18 O_lunatum_AY280466_AUSTRIA, 19 O_lunatum_AY280467_AUSTRIA, 20 O_fusiforme_AY280462_AZERBAIJAN, 21 O_fusiforme_AY280461_AZERBAIJAN, 22 O_fusiforme_AY280463_AZERBAIJAN, 23 O_cf_abietinum_HM031568_RUSSIA, 24 Ophiostoma_stenoceras_DQ296074_T, 25 O_stenoceras; TREE PAUP_1 = ((24:0.0,25:0.0):15.5,(23:1.0,((16:0.0,17:0.0,18:0.0,19:0.0,(20:0.0,21:0.0,22:0.0):1.0):1.0,(9:0.0,10:0.0,13:2.0,14:0.0,15:0.0,(4:0.0,5:0.0):2.0,(11:0.0,12:0.0):1.0,(1:0.0,2:0.0,3:0.0):2.0,(6:0.0,7:0.0,8:0.0):1.0):1.0):2.0):15.5):0.0; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 242; END; begin paup; exclude uninf; hsearch swap = tbr addseq = random nreps = 100; roottrees rootmethod = outgroup outroot = monophyl; showtrees; savetree file = filename.tre format = altnexus root = yes brlens = yes; pscores . / tl = yes ci = yes ri = yes; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 242; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 242; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1332939289593; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 2077875426833139204; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 8846721828272623544; mqVersion 275; checksumv 0 3 662364637 null getNumChars 242 numChars 242 getNumTaxa 25 numTaxa 25 short true bits 1152921504606846991 states 15 sumSquaresStatesOnly 114766.0 sumSquares -1.627925164504868E21 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 249; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1280 626; setLocation -4 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #2077875426833139204 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 876.1332939250687.6512284483994550243; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1031 559; setLocation -4 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; 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; 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; 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 #8846721828272623544 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 207; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1031 559; setLocation -4 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; 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; factory; exclude uninf; begin paup; bootstrap nreps = 1000; savetree file = pnbootstrap.tre format = altnexus from = 1 to = 1 savebootp = both maxdecimals = 0; END;