#NEXUS [written Sat Apr 28 19:55:43 UYT 2012 by Mesquite version 2.75 (build 564) at usuario-HP/192.168.1.7] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=16; TAXLABELS 'Teratosphaeria nubilosa CMW 3282 ex-epitype Victoria(Group C)' 'Teratosphaeria nubilosa CMW 26014 South Africa(Group C)' 'Teratosphaeria nubilosa CMW 26218 Uruguay(Group C)' 'Teratosphaeria nubilosa CMW 30900 Brazil(Group C)' 'Teratosphaeria nubilosa CMW 30714 NSW(Group C)' 'Teratosphaeria nubilosa CMW 30752 Victoria(Group C)' 'Teratosphaeria nubilosa CMW 30751 Victoria(Group C)' 'Teratosphaeria nubilosa CMW 30715 NSW(Group C)' 'Teratosphaeria nubilosa CMW 30707 NSW(Group A)' 'Teratosphaeria nubilosa CMW 30709 NSW(Group A)' 'Teratosphaeria nubilosa CMW 30717 NSW(Group A)' 'Teratosphaeria nubilosa CMW 30735 Tasmania(Group B)' 'Teratosphaeria nubilosa CMW 30723 WA(Group B)' 'Teratosphaeria nubilosa CMW 30745 Victoria(Group B)' 'Teratosphaeria nubilosa CMW 30750 Vicoria(Group B)' 'Teratosphaeria nubilosa CMW 31008 New Zealand(Group B)' ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=120; FORMAT DATATYPE = DNA INTERLEAVE GAP = - MISSING = ?; MATRIX 'Teratosphaeria nubilosa CMW 3282 ex-epitype Victoria(Group C)' AAGGTCTGTTCAAGCTCACGCGAAGGGCTGGACGTATTTTGCGCTTTCGCCTGTCAAGACCAGTGCGATGTGCCTGTCCACGACAGTCAAATTACTTCATGCCTAGGCAACGGAAATGGT 'Teratosphaeria nubilosa CMW 26014 South Africa(Group C)' AAGGTCTGTTCAAGCTCACGCGAAGGGCTGGACGTATTTTGCGCTTTCGCCTGTCAAGACCAGTGCGATGTGCCTGTCCACGACACTCAAATTACTTCATGCCTAGGCAACGGAAATGGT 'Teratosphaeria nubilosa CMW 26218 Uruguay(Group C)' AAGGTCTGTTCAAGCTCACGCGAAGGGCTGGACGTATTTTGCGCTTTCGCCTGTCAAGACCAGTGCGATGTGCCTGTCCACGACACTCAAATTACTTCATGCCTAGGCAACGGAAATGGT 'Teratosphaeria nubilosa CMW 30900 Brazil(Group C)' AAGGTCTGTTCAAGCTCACGCGAAGGGCTGGACGTATTTTGCGCTTTCGCCTGTCAAGACCAGTGCGATGTGCCTGTCCACGACACTCAAATTACTTCATGCCTAGGCAACGGAAATGGT 'Teratosphaeria nubilosa CMW 30714 NSW(Group C)' AAGGTCTGTTCAAGCTCACGCGAAGGGCTGGACGTATTTTGCGCTTTCGCCTGTCAAGACCAGTGCGATGTGCCTGTCCACGACAGTCAAATTACTTCATGCCTAGGCAACGGAAATGGT 'Teratosphaeria nubilosa CMW 30752 Victoria(Group C)' AAGGTCTGTTCAAGCTCACGCGAAGGGCTGGACGTATTTTGCGCTTTCGCCTGTCAAGACCAGTGCGATGTGCCTGTCCACGACAGTCAAATTACTTCATGCCTAGGCAACGGAAATGGT 'Teratosphaeria nubilosa CMW 30751 Victoria(Group C)' AAGGTCTGTTCAAGCTCACGCGAAGGGCTGGACGTATTTTGCGCTTTCGCCTGTCAAGACCAGTGCGATGTGCCTGTCCACGACAGTCAAATTACTTCATGCCTAGGCAACGGAAATGGT 'Teratosphaeria nubilosa CMW 30715 NSW(Group C)' AAGGTCTGTTCAAGCTCACGCGAAGGGCTGGACGTATTTTGCGCTTTCGCCTGTCAAGACCAGTGCGATGTGCCTGTCCACGACACTCAAATTACTTCATGCCTAGGCAACGGAAATGGT 'Teratosphaeria nubilosa CMW 30707 NSW(Group A)' AAGGTCTGTTCAAGCTCACGCGAAGGGCTGGACGTATTTTGCGCTTTCGCCTGTCAAGACCAGTGCGATGTGCCTGTCCACGACAGTCAAATTACTTCATGCCTAGGCAACGGAAATGGT 'Teratosphaeria nubilosa CMW 30709 NSW(Group A)' AAGGTCTGTTCAAGCTCACGCGAAGGGCTGGACGTATTTTGCGCTTTCGCCTGTCAAGACCAGTGCGATGTGCCTGTCCACGACAGTCAAATTACTTCATGCCTAGGCAACGGAAATGGT 'Teratosphaeria nubilosa CMW 30717 NSW(Group A)' AAGGTCTGTTCAAGCTCACGCGAAGGGCTGGACGTATTTTGCGCTTTCGCCTGTCAAGACCAGTGCGATGTGCCTGTCCAAGACAGTCAAATTACTTCATGCCTAGGCAACGGAAATGGT 'Teratosphaeria nubilosa CMW 30735 Tasmania(Group B)' AAGGTCTGTTCAAGCTCACGCGAAGGGCTGGACGTATTTTGCGCTTTCGCCTGTCAAGACCAGTGCGATGTGCCTGTCCACGACAGTCAAATTACTTCATGCCTAGGCAACGGAAATGGT 'Teratosphaeria nubilosa CMW 30723 WA(Group B)' AAGGTCTGTTCAAGCTCACGCGAAGGGCTGGACGTATTTTGCGCTTTCGCCTGTCAAGACCAGTGCGATGTGCCTGTCCACGACAGTCAAATTACTTCATGCCTAGGCAACGGAAATGGT 'Teratosphaeria nubilosa CMW 30745 Victoria(Group B)' AAGGTCTGTTCAAGCTCACGCGAAGGGCTGGACGTATTTTGCGCTTTCGCCTGTCAAGACCAGTGCGATGTGCCTGTCCACGACAGTCAAATTACTTCATGCCTAGGCAACGGAAATGGT 'Teratosphaeria nubilosa CMW 30750 Vicoria(Group B)' AAGGTCTGTTCAAGCTCACGCGAAGGGCTGGACGTATTTTGCGCTTTCGCCTGTCAAGACCAGTGCGATGTGCCTGTCCACGACAGTCAAATTACTTCATGCCTAGGCAACGGAAATGGT 'Teratosphaeria nubilosa CMW 31008 New Zealand(Group B)' AAGGTCTGTTCAAGCTCACGCGAAGGGCTGGACGTATTTTGCGCTTTCGCCTGTCAAGACCAGTGCGATGTGCCTGTCCACGACAGTCAAATTACTTCATGCCTAGGCAACGGAAATGGT ; END; BEGIN TREES; Title 'Trees from "tn4mes.txt"'; LINK Taxa = Taxa; TRANSLATE 1 'Teratosphaeria nubilosa CMW 3282 ex-epitype Victoria(Group C)', 2 'Teratosphaeria nubilosa CMW 26014 South Africa(Group C)', 3 'Teratosphaeria nubilosa CMW 26218 Uruguay(Group C)', 4 'Teratosphaeria nubilosa CMW 30900 Brazil(Group C)', 5 'Teratosphaeria nubilosa CMW 30714 NSW(Group C)', 6 'Teratosphaeria nubilosa CMW 30752 Victoria(Group C)', 7 'Teratosphaeria nubilosa CMW 30751 Victoria(Group C)', 8 'Teratosphaeria nubilosa CMW 30715 NSW(Group C)', 9 'Teratosphaeria nubilosa CMW 30707 NSW(Group A)', 10 'Teratosphaeria nubilosa CMW 30709 NSW(Group A)', 11 'Teratosphaeria nubilosa CMW 30717 NSW(Group A)', 12 'Teratosphaeria nubilosa CMW 30735 Tasmania(Group B)', 13 'Teratosphaeria nubilosa CMW 30723 WA(Group B)', 14 'Teratosphaeria nubilosa CMW 30745 Victoria(Group B)', 15 'Teratosphaeria nubilosa CMW 30750 Vicoria(Group B)', 16 'Teratosphaeria nubilosa CMW 31008 New Zealand(Group B)'; TREE PAUP_1 = (1:100.0,(2:100.0,3:100.0,4:100.0,8:100.0)65:65.0,5:100.0,6:100.0,7:100.0,9:100.0,10:100.0,11:100.0,12:100.0,13:100.0,14:100.0,15:100.0,16:100.0)0; END; Begin paup; set criterion = parsimony storebrlens = yes; hsearch swap = tbr; bootstrap nreps = 1000; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 120; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 120; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 120; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1335653743641; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 2929191329609454278; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 132220965019951025; mqVersion 275; checksumv 0 3 3071213807 null getNumChars 120 numChars 120 getNumTaxa 16 numTaxa 16 short true bits 15 states 15 sumSquaresStatesOnly 41229.0 sumSquares 41229.0 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 700 464; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #2929191329609454278 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #2929191329609454278; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 600 397; setLocation 8 8; 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.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #132220965019951025 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 600 397; setLocation 8 8; 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;