#NEXUS [written Tue Nov 09 14:51:05 CST 2010 by Mesquite version 2.72 (build 527) at JuliusOffice-PC/199.17.31.244] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=16; TAXLABELS Stephanodiscus_hantzschii Stephanodiscus_minutus Stephanodiscus_vestibulis Stephanodiscus_carconensis 'Stephanodiscus subtransilvanicus (African Fossil)' 'Stephanodiscus subtransilvanicus (Laurentian Great Lakes)' Stephanodiscus_agassizensis Stephanodiscus_alpinus Stephanodiscus_neoastraea Stephanodiscus_galileensis Stephanodsicus_rotula Stephanodiscus_niagarae Stephanodiscus_reimerii Stephanodiscus_yellowstonensis Stephanodiscus_superiorensis Stephanodiscus_kusuensis ; END; BEGIN CHARACTERS; TITLE 'Matrix in file "mike_matrix.nex"'; DIMENSIONS NCHAR=24; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2 3 4"; MATRIX Stephanodiscus_hantzschii 0000000011000020?1100000 Stephanodiscus_minutus 000100001100010001100000 Stephanodiscus_vestibulis 000100101100010001001100 Stephanodiscus_carconensis 0000000110011320?1100012 'Stephanodiscus subtransilvanicus (African Fossil)' 0000000111000100?1100012 'Stephanodiscus subtransilvanicus (Laurentian Great Lakes)'0000000110000100?0100012 Stephanodiscus_agassizensis 101200001100010001000001 Stephanodiscus_alpinus 101000001100010001000001 Stephanodiscus_neoastraea 1020100010000100?1100002 Stephanodiscus_galileensis 102310001000010111100002 Stephanodsicus_rotula 212310001000011001100002 Stephanodiscus_niagarae 213210001000111001100002 Stephanodiscus_reimerii 213210001000111001110002 Stephanodiscus_yellowstonensis 214211101000111001100002 Stephanodiscus_superiorensis 213110001010121001100002 Stephanodiscus_kusuensis 213310001000111001100002 ; END; BEGIN TREES; Title 'Trees from "mike_matrix.nex"'; LINK Taxa = Taxa; TRANSLATE 1 Stephanodiscus_hantzschii, 2 Stephanodiscus_minutus, 3 Stephanodiscus_vestibulis, 4 Stephanodiscus_carconensis, 5 'Stephanodiscus subtransilvanicus (African Fossil)', 6 'Stephanodiscus subtransilvanicus (Laurentian Great Lakes)', 7 Stephanodiscus_agassizensis, 8 Stephanodiscus_alpinus, 9 Stephanodiscus_neoastraea, 10 Stephanodiscus_galileensis, 11 Stephanodsicus_rotula, 12 Stephanodiscus_niagarae, 13 Stephanodiscus_reimerii, 14 Stephanodiscus_yellowstonensis, 15 Stephanodiscus_superiorensis, 16 Stephanodiscus_kusuensis; TREE 'UNTITLED+' = (1,((2,3),(((4,6),5),((7,8),(9,(10,(11,(12,13,15,14)))))))); END; BEGIN ASSUMPTIONS; OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS; TYPESET * UNTITLED = unord: 1 - 24; END; BEGIN MacClade; Version 4.0 81; LastModified -1089011606; FileSettings editor '0' '0' '1' '1'; Singles 010; Editor 0001100111111110010001001 '0' '24' Geneva '9' '268' '1' all; EditorPosition '40' '4' '723' '1011'; TreeWindowPosition '40' '2' '728' '1018'; ListWindow Characters closed Geneva '9' '50' '10' '121' '352' 000; ListWindow Taxa closed Geneva '9' '50' '12' '297' '371' 100; ListWindow Trees closed Geneva '9' '50' '10' '121' '379'; ListWindow TypeSets closed Geneva '9' '50' '10' '276' '490'; ListWindow WtSets closed Geneva '9' '50' '10' '276' '490'; ListWindow ExSets closed Geneva '9' '50' '10' '276' '490'; ListWindow CharSets closed Geneva '9' '50' '10' '276' '490'; ListWindow TaxSets closed Geneva '9' '50' '10' '276' '490'; ListWindow CharPartitions closed Geneva '9' '50' '10' '276' '490'; ListWindow CharPartNames closed Geneva '9' '50' '10' '276' '490'; ListWindow WtSets closed Geneva '9' '50' '10' '276' '490'; ChartWindowPosition '50' '30' '688' '964'; StateNamesSymbols closed Geneva '9' '10' '50' '30' '148' '220'; WindowOrder Data; OtherSymbols & / 00 ? -; Correlation '0' '0' '1000' '0' '0' 10011010; Salmo 00000001; EditorFile '2'; ExportHTML _ MOSS '100' 110000; PrettyPrint 10; EditorToolsPosition '605' '44' '115' '165'; TreeToolsPosition '607' '5' '126' '138'; TreeWindowProgram 10; TreeWindow 0000; Continuous '0' '3' 1; Calculations 0000001; SummaryMode '0' '0' 0; Charts Geneva '9' ( normal ) 0010; NexusOptions '0' '0' '50' 001011011; TipLabel '1'; TreeFont Geneva '32' ( normal ); TreeShape 1.0 1.0 0100; TraceLabels 0101; ChartColors '0' '0' '65535' '9' '0' 1; ChartBiggestSpot 1; ChartPercent 10; ChartBarWidth '10' 1; ChartVerticalAxis 10101; ChartMinMax '0'; TraceAllChangesDisplay '1' 1; BarsOnBranchesDisplay '0' '0' '60000' '10000' '10000' '10000' '10000' '60000' '65000' '65000' '65000' '6' '1' 0000101; ContinuousBranchLabels 0; AllStatesBranchLabels 1; IndexNotation '2' 1; PrintTree 10.00 '2' '2' '2' '2' '2' '2' '2' '2' '2' '2' '2' Geneva '9' ( normal ) Geneva '10' ( normal ) Geneva '9' ( normal ) Geneva '9' ( normal ) Geneva '9' ( bold ) Geneva '9' ( normal ) Geneva '9' ( normal ) '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '1' '1' '1' '1' '-32703' '3' '-39' '4' '-40' '0' '1' '2' '1' '8' '0' '0' '0' '2' 1000111000000000000100000111000; MatchChar 00 .; EntryInterpretation 01; ColorOptions 0; TreeTools '0' '5' '4' '0' '10' '4' '0' 00100111111101110; EditorTools '0' '0' '0' '1000' '0' '0' '6' '3' '0' 100000101110001; PairAlign '2' '2' '3' '2' '1' '1' '2' '1' '3' 1010; BothTools '1'; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 24; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1289335865635; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 6260251169378428030; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 3529716428497818872; checksumv 0 2 2655063552 null numChars 24 short true bits 31 states 31 sumSquaresStatesOnly 1891.0 NumFiles 1 NumMatrices 1; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1407 729; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #6260251169378428030 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 836.1289335623046.3641692326142214225; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1307 662; setLocation 8 8; 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 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; setTree '(1,((2,3),(((4,6),5),((7,8),(9,(10,(11,(12,13,15,14))))))));'; 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.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #3529716428497818872 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1307 662; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; endTell; setActive; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; colorCells #mesquite.charMatrices.NoColor.NoColor; 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 on; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames on; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleAllowAutosize on; toggleColorsPanel off; toggleDiagonal on; setDiagonalHeight 80; 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.categ.SmallStateNamesEditor.SmallStateNamesEditor; tell It; panelOpen true; endTell; endTell; endTell; endTell; end;