#NEXUS [written Thu Mar 06 10:57:43 CST 2014 by Mesquite version 2.75 (build 564) at 144-236.mccollum.uni.edu/134.161.144.236] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=14; TAXLABELS Orthogeomys_lanius_CNMA46483 Orthogeomys_lanius_CNMA46463 Orthogeomys_lanius_FMNH13836 Orthogeomys_hispidus_LSUMZ36767 Orthogeomys_hispidus_LSUMZ36090 Orthogeomys_hispidus_CNMA41025 Orthogeomys_hispidus_LSUMZ36761 Orthogeomys_hispidus_CMNH112140 Orthogeomys_grandis_LSUMZ34392 Orthogeomys_grandis_CMNH112150 Orthogeomys_heterodus_LSUMZ29261 Orthogeomys_dariensis_LSUMZ25434 Geomys_breviceps_LSUMZ29336 Thomomys__bulbivorus_TSD535 ; END; BEGIN CHARACTERS; TITLE 'Matrix in file "359cybdta.nex"'; DIMENSIONS NCHAR=359; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Orthogeomys_lanius_CNMA46483 ATGACAATTATACGAAAATCACACCCACTAATAAAAATTGTCAACCATGCTTTCATTGACCTACCAACACCACCTAATATCTCAGGTTGATGAAACTTCGGCTCCCTATTAGGACTATGCTTAATCCTACAAATCTCAACAGGCCTATTTCTAGCAATACATTACACATCTGATACACTTACAGCCTGATTAATCCGACATATACATGCCAACGGCGCCTCCTTATTCTTCATTTGTATTTATATCCACATCGGACGAGGAATCTACTACGGATCCTATCTTTACACAGAAACATGAAACATCGGCATTTTACTGTTATTTCTAACTATAGCCACTGCATTCGTAGGATATGTACTACC Orthogeomys_lanius_CNMA46463 ATGACAATTATACGAAAATCACACCCACTAATAAAAATTGTCAACCATGCTTTCATTGACCTACCAACACCACCTAATATCTCAGGTTGATGAAACTTCGGCTCCCTATTAGGACTATGCTTAATCCTACAAATCTCAACAGGCCTATTTCTAGCAATACATTACACATCTGATACACTTACAGCCTGATTAATCCGACATATACATGCCAACGGCGCCTCCTTATTCTTCATTTGTATTTATATCCACATCGGACGAGGAATCTACTACGGATCCTATCTTTACACAGAAACATGAAACATCGGCATTTTACTGTTATTTCTAACTATAGCCACTGCATTCGTAGGATATGTACTACC Orthogeomys_lanius_FMNH13836 ATGACAATTATACGAAAATCACACCCACTAATAAAAATTGTCAACCATGCTTTCATTGACCTACCAACACCACCTAATATCTCAGGTTGATGAAACTTCGGCTCCCTATTAGGACTATGCTTAATCCTACAAATCTCAACAGGCCTATTTCTAGCAATACATTACACATCTGATACACTCACAGCCTGATTAATCCGACATATACATGCCAACGGCGCCTCCTTATTCTTCATTTGTATTTATATCCACATCGGACGAGGAATCTACTACGGATCCTATCTTTACACAGAAACATGAAACATCGGCATTTTACTGTTATTTCTAACTATAGCCACTGCATTCGTAGGATATGTACTACC Orthogeomys_hispidus_LSUMZ36767 ATGGCAATTATACGAAAATCTCACCCACTAATAAAAATTGTCAACCATGCTTTCATTGACCTACCAACACCACCTAACATCTCAGGTTGATGAAATTTCGGCTCCCTATTAGGACTATGCTTAATTCTACAAATCTCTACAGGCCTATTTCTAGCAATACACTACACATCTGACACACTTACAGCCTGATTAATCCGATATATACATGCCAACGGCGCCTCCCTATTCTTCATTTGCCTTTATATTCACATCGGACGAGGAATTTACTATGGATCCTATCTTTATACAGAAACATGAAACATCGGCATTTTACTACTATTTTTAACTATAGCCACTGCATTCGTAGGATATGTACTACC Orthogeomys_hispidus_LSUMZ36090 ATGGCAATTATACGAAAATCTCACCCACTAATAAAAATTGTCAACCATGCTTTCATTGACCTACCAACACCACCTAATATCTCAGGTTGATGAAATTTCGGCTCCCTATTAGGACTATGCTTAATTCTACAAATCTCTACAGGCCTATTTCTAGCAATACACTACACATCTGACACACTCACAGCCTGATTAATCCGATATATACATGCTAACGGCGCCTCCCTATTCTTCATTTGCCTTTATATTCACATCGGACGAGGAATCTACTATGGATCCTATCTTTATACAGAAACATGAAACATCGGTATTTTATTGCTATTTTTAACTATAGCCACTGCATTCGTGGGATATGTACTACC Orthogeomys_hispidus_CNMA41025 ATGACAATTATACGAAAATCTCACCCACTAATAAAAATTGTCAACCATGCTTTCATTGACCTACCAACACCACCTAATATCTCAGGTTGATGAAATTTCGGCTCCCTATTAGGACTATGCTTAATTCTACAAATCTCTACAGGCCTATTTCTAGCAATACACTACACATCTGACACACTTACAGCCTGATTAATCCGATACATACATGCCAACGGCGCCTCCCTATTCTTCATTTGCCTTTATATTCACATCGGACGAGGAATTTACTATGGATCCTATCTTTATACAGAAACATGAAACATCGGCATTTTATTACTATTTTTAACTATAGCCACTGCATTCGTAGGATACGTACTACC Orthogeomys_hispidus_LSUMZ36761 ATGACAATTATACGAAAATCTCACCCACTAATAAAAATTGTCAACCATGCTTTCATTGACCTACCAACACCACCTAATATCTCAGGTTGATGAAATTTCGGCTCCCTATTAGGACTATGCTTAATTCTACAAATCTCTACAGGCCTATTTCTAGCAATACACTACACATCTGACACACTTACAGCCTGATTAATCCGATACATACATGCCAACGGCGCCTCCCTATTCTTCATTTGCCTTTATATTCACATCGGACGAGGAATTTACTATGGATCCTATCTTTATACAGAAACATGAAACATCGGCATTTTATTACTATTTTTAACTATAGCCACTGCATTCGTAGGATATGTACTACC Orthogeomys_hispidus_CMNH112140 ATGACAATTATACGAAAATCCCACCCACTAATAAAAATTGTCAACCATGCTTTCATTGACCTACCAACACCACCCAATATCTCAGGTTGATGAAATTTCGGCTCCCTATTAGGACTATGCTTAATTCTACAAATCTCTACAGGCCTATTTCTAGCAATACACTACACATCTGACACACTTACAGCCTGATTAATCCGATACATACATGCCAACGGCGCCTCCCTATTCTTCATTTGCCTTTATATTCACATCGGACGAGGAATTTACTATGGATCCTACCTTTATACAGAAACATGAAACATCGGCATTTTATTACTATTCTTAACTATAGCCACTGCATTCGTAGGATATGTACTACC Orthogeomys_grandis_LSUMZ34392 ATGACAATCCTACGAAAATCACACCCTTTAATAAAAATTGTCAACCATGCTTTCATCGACCTACCAACACCCCCTAACATCTCCAGTTGATGAAATTTTGGTTCCCTATTAGGACTATGTCTAACCCTTCAAATCTTAACAGGCTTATTCTTAGCAATACACTACACATCAGACACCCTCACAGCTTGATTAATTCGATACATACATGCCAATGGCGCTTCCCTATTCTTCATCTGCCTCTACATCCATATCGGACGAGGTATCTACTATGGATCTTATTTATACTCAGAAACATGAAACATTGGAATCCTGCTACTATTCCTAACTATAGCAACTGCATTTGTGGGTTACGTACTACC Orthogeomys_grandis_CMNH112150 ATGACAATCCTACGAAAATCACATCCTTTAATAAAAATTGTCAACCACGCTTTCATCGATCTACCAACACCCCCTAACATCTCCAGTTGATGAAATTTCGGTTCCCTATTAGGACTATGTTTAATCCTTCAAATCTTAACAGGCTTATTTTTAGCAATACACTACACATCAGACACTCTCACGGCTTGATTAATCCGATACATACATGCCAACGGCGCTTCCCTATTCTTCATCTGCCTATATATCCATATCGGACGAGGCATCTACTACGGATCCTACCTATATTCAGAAACATGAAATATTGGAATCTTACTATTACTCCTAACTATGGCAACTGCATTTATAGGCTACGTACTACC Orthogeomys_heterodus_LSUMZ29261 ACGACAATGATACGAAAATCCCATCCACTAATAAAAATTGTTAACCATGCTTTCATCGACTTACCAACACCACCCAACATCTCAGGATGATGAAACTTTGGTTCCCTGCTAGGACTATGCTTAATTTTACAAATTTCAACAGGCCTATTTTTAGCAATACACTACACGTCAGACACACTTACAGCTTGATTAATCCGATATATACATGCCAACGGTGCCTCCCTATTCTTCATTTGCCTCTACATTCACATCGGACGAGGCATTTACTATGGGTCCTACCTCTATAAAGAAACATGAAATATCGGCATTTTATTACTATTTTTAACTATAGCCACTGCATTCATAGGATATGTACTGCC Orthogeomys_dariensis_LSUMZ25434 ATGACAATAATACGAAAATCCCATCCGCTTATAAAAATTGTCAACCATGCTTTCATCGACCTACCAACACCACCCAACATTTCCGGATGATGAAACTTTGGCTCCCTACTAGGACTATGCTTAATCTTACAAATCTCAACAGGCCTATTTTTAGCAATACACTATACGTCAGACACACTTACAGCTTGATTAATCCGATATCTACATGCCAATGGTGCCTCCCTATTCTTCATTTGCCTTTACATTCACATCGGACGAGGAATTTACTACGGATCTTATCTTTATACAGAAACATGGAATATAGGCATTTTACTGCTATTCTTAACTATAGCCACTGCATTCATAGGATATGTGCTGCC Geomys_breviceps_LSUMZ29336 ATGGCAGTTATACGAAAATCACACCCCTTAATAAAAATTGTCAACCACGCATTCATCGACCTACCAACTCCCCCTAATATTTCTGGCTGATGAAATTTTGGCTCCCTATTGGGTCTGTGCTTAATTCTTCAAATCCTAACAGGCTTATTTCTAGCAATACACTACACATCGGACACTCTCACAGCTTGACTCATCCGATATATGCACGCCAACGGAGCTTCTCTATTCTTCATCTGTCTATATATCCACATCGGACGAGGTATTTACTACGGATCTTATCTATACACAGAAACATGAAATATCGGCATCCTACTGCTATTCCTAACCATAGCCACTGCTTTCGTAGGCTACGTATTACC Thomomys__bulbivorus_TSD535 ATGAAAATTATACGCAAGTCCCATCCGTTATTTAAAATCGTAAATCATGCCTTTATTGACTTACCTACCCCACCTAATATTTCAGGTTGATGAAATTTTGGCTCTCTCTTAGGTATATGCTTGATCCTACAAATCTCAACTGGCCTATTCTTAGCCATACACTATACATCTGACACCCTAACAGCTTGATTAATCCGATATATACATGCAAATGGAGCATCACTATTCTTCATCTGCTTATATATACACATTGGTCGTGGTATCTACTATGGCTCCTACCTTTATAAGGAAACATGAAATATTGGCATCTTGCTCCTATTCTTATCAATAGCTACAGCATTCGTTGGTTACGTACTACC ; END; BEGIN TREES; Title 'Trees from "359.nex"'; LINK Taxa = Taxa; TRANSLATE 1 Orthogeomys_lanius_CNMA46483, 2 Orthogeomys_lanius_CNMA46463, 3 Orthogeomys_lanius_FMNH13836, 4 Orthogeomys_hispidus_LSUMZ36767, 5 Orthogeomys_hispidus_LSUMZ36090, 6 Orthogeomys_hispidus_CNMA41025, 7 Orthogeomys_hispidus_LSUMZ36761, 8 Orthogeomys_hispidus_CMNH112140, 9 Orthogeomys_grandis_LSUMZ34392, 10 Orthogeomys_grandis_CMNH112150, 11 Orthogeomys_heterodus_LSUMZ29261, 12 Orthogeomys_dariensis_LSUMZ25434, 13 Geomys_breviceps_LSUMZ29336, 14 Thomomys__bulbivorus_TSD535; TREE tree_1 = ((((((6:0.00274186,7:5.144E-5):0.00723304,8:0.01664953,4:0.00756875,5:0.01610754):0.00889719,(3:0.00218737,(1:0.0,2:0.0):6.0594E-4):0.03835745):0.02071534,(11:0.04427237,12:0.04246435):0.02879371):0.02171997,(13:0.08973366,(9:0.04695882,10:0.03758518):0.04151684):0.01712243):0.02277789,14:0.12963397); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 359; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 359; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 359; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1394125063096; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 3269197719778445125; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 6177290938805202532; mqVersion 275; checksumv 0 3 743177096 null getNumChars 359 numChars 359 getNumTaxa 14 numTaxa 14 short true bits 15 states 15 sumSquaresStatesOnly 115591.0 sumSquares 115591.0 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 1099 597; setLocation 410 102; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #3269197719778445125 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #3269197719778445125; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 999 530; setLocation 410 102; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.ibeam; 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 #3269197719778445125 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1671.1394124342400.8694243153949236896; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 999 530; setLocation 410 102; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.collapse; 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; 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 #6177290938805202532 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 999 530; setLocation 410 102; 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;