#NEXUS [written Fri Oct 21 17:14:55 CEST 2011 by Mesquite version 2.75 (build 564) at fli-tue-pc324/172.20.47.5] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=13; TAXLABELS Canis_familaris_CEACAM1 Canis_familaris_CEACAM23 Canis_familaris_CEACAM24 Canis_familaris_CEACAM25 Canis_familaris_CEACAM28 Canis_familaris_CEACAM29 Canis_familaris_CEACAM30 Homo_sapiens_CEACAM1 Homo_sapiens_CEACAM3 Homo_sapiens_CEACAM5 Homo_sapiens_CEACAM6 Homo_sapiens_CEACAM19 Canis_familaris_CEACAM19 ; END; BEGIN CHARACTERS; TITLE 'Comparison of dog and human CEACAMs.txt"'; DIMENSIONS NCHAR=330; FORMAT DATATYPE = DNA INTERLEAVE GAP = - MISSING = ?; MATRIX Canis_familaris_CEACAM1 CAAGTCACTGTGGAGTCCGTGCCTCCCAATGCTGCTGAAGGGA--AGGACGCTCTTCTGCGGGTCCTCAATCTGCCTG Canis_familaris_CEACAM23 CAAGTCACTGTGGAATCCGTGCCTCCCAATGCTGCTGAAGGGA--AGGACGCTCTTCTGCGGGTCCTCAATTTGCCTG Canis_familaris_CEACAM24 CAAGTCACTGTGGAATCCGTGCCTCCCAATGCTGCTGAAGGGA--AGGACGCTCTTCTGCGGGTCCTCAATCTGCCTG Canis_familaris_CEACAM25 CAAGTCACTGTGGAGTCGGTGCCTCCCAATGCTGCTGAAGGGA--AGGACGTTCTTCTGCGAGTCCTCAATCTGCCTG Canis_familaris_CEACAM28 CAAGTCACTGTGGAGTCCGTGCCTCCCAATGCTGCTGAAGGGA--AGGATGCTCTTCTGCGGGTCCTCAATCTGCCTG Canis_familaris_CEACAM29 CAAGTCACTGTGGAGTCCGTGCCTCCCAATGCTGCTGAAGGGA--AGGATGCTCTTCTGCGGGTCCTCAATCTGCCTG Canis_familaris_CEACAM30 CAAGTCACTGTGGAGTCTGTGCCTCCCAATGCTGCTGAAGGGA--AGGATGCTCTTCTGCGGGTCCTCAATCTGCCTG Homo_sapiens_CEACAM1 CAGCTCACTACTGAATCCATGCCATTCAATGTTGCAGAGGGGA--AGGAGGTTCTTCTCCTTGTCCACAATCTGCCCC Homo_sapiens_CEACAM3 AAGCTCACTATTGAATCCATGCCGCTCAGTGTCGCAGAGGGGA--AGGAGGTGCTTCTACTTGTCCACAATCTGCCCC Homo_sapiens_CEACAM5 AAGCTCACTATTGAATCCACGCCGTTCAATGTCGCAGAGGGGA--AGGAGGTGCTTCTACTTGTCCACAATCTGCCCC Homo_sapiens_CEACAM6 AAGCTCACTATTGAATCCACGCCGTTCAATGTCGCAGAGGGGA--AGGAGGTTCTTCTACTCGCCCACAACCTGCCCC Homo_sapiens_CEACAM19 CAGCTCTCTACATCCAGAAGATTCCAGAGCAGCCTCAAAAGAACCAGGACCTTCTCCTGTCAGTCCAGGGTGTCCCAG Canis_familaris_CEACAM19 CTGCCCTACGCATCCAGAAGATTCCAGAGTATCCTCAAAAAGACCAGGACCTTCTCCTGTCTGTCCAGGGCATCCCAG Canis_familaris_CEACAM1 GGGATACAGCAAGCCTTACCTGGTTCAAAGGGGAAACTGTATTGCCGACCCATAAAATTCTATTATATGTAATAGACA Canis_familaris_CEACAM23 GGGATACAGCAGGCCTTACCTGGTTCAGAGGGGAAATTGTAGCACCTGTCCATCAAATTGTATTATATGTAGTAGACA Canis_familaris_CEACAM24 GGGATACAGCAGGCCTTACCTGGTTCAGAGGGGAAATTGTAGCACCTGTCCATCAAATTGTATTATATGTAGTAGACA Canis_familaris_CEACAM25 GGGATCTTCTAGGATATGCCTGGTTCAGAGGGAAAAGTGTAGAGACCAATAATCGTATTGTGTCATATGTGGTAAACA Canis_familaris_CEACAM28 GGGATACAGCAAGCCTTACCTGGTTCAAAGGGGAAACTGTATTGCCGACCCATAAAATTCTATTATATGTAATAGACA Canis_familaris_CEACAM29 GGGATACAGCAGGCCTTACCTGGTTCAGAGGGGAAACTGTATTGCCGACCCATAAAATTCTATTATATGTAATAGACA Canis_familaris_CEACAM30 GGGATACAGCAAGCCTTACCTGGTTCAGAGGGGAAACTGCATTGCCGACCCATAAAATTCTATTATATGTAATAGACA Homo_sapiens_CEACAM1 AGCAACTTTTTGGCTACAGCTGGTACAAAGGGGAAAGAGTGGATGGCAACCGTCAAATTGTAGGATATGCAATAGGAA Homo_sapiens_CEACAM3 AGCATCTTTTTGGCTACAGCTGGTACAAAGGGGAAAGAGTGGATGGCAACAGTCTAATTGTAGGATATGTAATAGGAA Homo_sapiens_CEACAM5 AGCATCTTTTTGGCTACAGCTGGTACAAAGGTGAAAGAGTGGATGGCAACCGTCAAATTATAGGATATGTAATAGGAA Homo_sapiens_CEACAM6 AGAATCGTATTGGTTACAGCTGGTACAAAGGCGAAAGAGTGGATGGCAACAGTCTAATTGTAGGATATGTAATAGGAA Homo_sapiens_CEACAM19 ACACCTTCCAGGACTTCAACTGGTACCTGGGGGAGGAGACGTACGGAGGCACGAGGCTATTTACCTACATCCCTGGGA Canis_familaris_CEACAM19 GCAACTTTCAGGACTTCAACTGGTACCTGGGGGAGGAGACCAATGGTGGCACGATGTTATTCACCTACTTCCCCGATC Canis_familaris_CEACAM1 CCAAAATCACTACCCCGGG-GCCTGCATACAGCGGCAGAGAGACAATATA-----CCCCAACGGATCCCTGCTATTCC Canis_familaris_CEACAM23 CACGAGTAATTACCCCGGG-GCCTGCACACAGTGGCAGAGAGATAATATA-----CCCCAATGGATCCCTGCTGTTCC Canis_familaris_CEACAM24 CACGAGTAATTGTCCCGGG-GCCTGCATACAGTGGCAGAGAGATAATATA-----CCCCAATGGATCCCTGCTGTTCC Canis_familaris_CEACAM25 CACAAGTGATTACCCCCGG-GCATGCACACAGCGGCAGAGAGACAGCATA-----CCCCAATGGATCCTTGCTGTTTC Canis_familaris_CEACAM28 CCAAAATCACTAACCCGGG-GCCTGCATACAGCGGCAGAGAGACAATATA-----CCCCAACGGATCCCTGCTGTTCC Canis_familaris_CEACAM29 CCAAAGTCACTACCCCGGG-GCCTGCATACAGCCACAGAGAGACAATATA-----CCCCAATGGATCCCTGCTGTTCC Canis_familaris_CEACAM30 CCAAAGTCACTACCCCGGG-GCCTGCATACAGCGGCAGAGAGACAATATA-----CCCCAACGGATCCCTGCTGTTCC Homo_sapiens_CEACAM1 CTCAACAAGCTACCCCAGG-GCCCGCAAACAGCGGTCGAGAGACAATATA-----CCCCAATGCATCCCTGCTGATCC Homo_sapiens_CEACAM3 CTCAACAAGCTACCCCAGG-GGCCGCATACAGCGGTCGAGAGACAATATA-----CACCAATGCATCCCTGCTGATCC Homo_sapiens_CEACAM5 CTCAACAAGCTACCCCAGG-GCCCGCATACAGTGGTCGAGAGATAATATA-----CCCCAATGCATCCCTGCTGATCC Homo_sapiens_CEACAM6 CTCAACAAGCTACCCCAGG-GCCCGCATACAGTGGTCGAGAGACAATATA-----CCCCAATGCATCCCTGCTGATCC Homo_sapiens_CEACAM19 TACAACGGCCTCAGAGGGATGGCAGTGCCATGGGACAGCGAGACATCGTGGGCTTCCCCAATGGTTCCATGCTGCTGC Canis_familaris_CEACAM19 TCCAGTGGCCCCAGAGGGACGGCAGTGCCATGGGACAGCATGACATCGTTGGCTTCCCCAATGGCTCCATGATGCTGC Canis_familaris_CEACAM1 AGAACATCACCCTGAACGACACTGGATCCTACATCCTACAAATCATAAACCAAAAATTTGAAACTGCACTAGTACGTG Canis_familaris_CEACAM23 AGAACATCACCCTGAGCGACACTGGATCCTACATCCTACAAATCATAAACAGAAAATTTGAAACTGCACTAGTAACTG Canis_familaris_CEACAM24 AGAATATCACCCTGAAAGACACTGGATCCTACATCCTACAAATCATAAACCAAAAATTTGAAACTGCACTAGTACCTG Canis_familaris_CEACAM25 AGAACATCACCCTGAAGGACACGGGGTACTACACCCTACAAATCATTACAAATGATGTTCAAGTTGAACAAGTACGTG Canis_familaris_CEACAM28 AGAACATCACCCTGAACGACACTGGATCCTACATCCTACAAATCATAAACCAAAAATTTGAAACTGCACTAATACGGG Canis_familaris_CEACAM29 AGAACATCACCGTGAATAATGCCGGATATTACATCCTACAAATCATAAACAGAAAATTTGAAACTGCACTAGTACCTG Canis_familaris_CEACAM30 AGAACATCACCCTGAATGATGCCGGATCCCACATCCTACAAATCATAAACCAAAAATTTGAAACTGCACTAATACGGG Homo_sapiens_CEACAM1 AGAACGTCACCCAGAATGACACAGGATTCTACACCCTACAAGTCATAAAGTCAGATCTTGTGAATGAAGAAGCAACTG Homo_sapiens_CEACAM3 AGAATGTCACCCAGAATGACATAGGATTCTACACCCTACAAGTCATAAAGTCAGATCTTGTGAATGAAGAAGCAACTG Homo_sapiens_CEACAM5 AGAACATCATCCAGAATGACACAGGATTCTACACCCTACACGTCATAAAGTCAGATCTTGTGAATGAAGAAGCAACTG Homo_sapiens_CEACAM6 AGAACGTCACCCAGAATGACACAGGATTCTATACCCTACAAGTCATAAAGTCAGATCTTGTGAATGAAGAAGCAACCG Homo_sapiens_CEACAM19 GCCGCGCCCAGCCTACAGACAGTGGCACCTACCAAGTAGCCATTACCATCAACTCTGAATGGACTATGAAGGCCAAGA Canis_familaris_CEACAM19 ATCGTGTCCAGCCCACCGACAGTGGCACCTACCAGGTAGCTGTCAACATCAATCCTGCCTGGATCATGAGGGCCAAGA Canis_familaris_CEACAM1 GACAGCTCCAAGTATTC- Canis_familaris_CEACAM23 GAGAGCTCCGAGTATTC- Canis_familaris_CEACAM24 GACAGCTCCGAGTATTC- Canis_familaris_CEACAM25 GACAGCTCCGAGTATTC- Canis_familaris_CEACAM28 GACAGCTCCAAGTATTC- Canis_familaris_CEACAM29 GACAGCTCCGAGTATTC- Canis_familaris_CEACAM30 GACAGCTCCGAGTATTC- Homo_sapiens_CEACAM1 GACAGTTCCATGTATAC- Homo_sapiens_CEACAM3 GACAGTTCCATGTATAC- Homo_sapiens_CEACAM5 GCCAGTTCCGGGTATAC- Homo_sapiens_CEACAM6 GACAGTTCCATGTATAC- Homo_sapiens_CEACAM19 CTGAGGTCCAGGTAGCTG Canis_familaris_CEACAM19 CTGAGGTCCAGGTGGCCG ; END; BEGIN TREES; Title Analysis_of_dog_and_human_CEACAMs; LINK Taxa = Taxa; TRANSLATE 1 Canis_familaris_CEACAM1, 2 Canis_familaris_CEACAM23, 3 Canis_familaris_CEACAM24, 4 Canis_familaris_CEACAM25, 5 Canis_familaris_CEACAM28, 6 Canis_familaris_CEACAM29, 7 Canis_familaris_CEACAM30, 8 Homo_sapiens_CEACAM1, 9 Homo_sapiens_CEACAM3, 10 Homo_sapiens_CEACAM5, 11 Homo_sapiens_CEACAM6, 12 Homo_sapiens_CEACAM19, 13 Canis_familaris_CEACAM19; TREE Imported_tree_0 = ((12:0.03717962,13:0.1611133)1.0000:0.51082572,((8:0.01871393,(10:0.03646244,(9:0.02261222,11:0.03854549)0.4320:0.00624102)0.7160:0.00936678)0.9640:0.15446885,(4:0.11827104,((2:0.0207641,3:0.01493516)0.9640:0.02552532,(6:0.02490097,(7:0.01341518,(1:0.01075428,5:0.00499642)0.6960:0.02010224)0.5660:0.01701827)0.9960:0.04874307)0.9900:0.07151406)0.7540:0.11563943):0.51082572); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 330; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 330; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 330; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1319210095607; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8544006335848417822; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 8835592963818847919; mqVersion 275; checksumv 0 3 2286358693 null getNumChars 330 numChars 330 getNumTaxa 13 numTaxa 13 short true bits 15 states 15 sumSquaresStatesOnly 79134.0 sumSquares 79134.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState true false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 700 467; setLocation 716 114; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #8544006335848417822 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 832.1319201199057.4320488141102426064; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -67; setLocation 716 114; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.reroot; 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; orientRight; 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 #8835592963818847919 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -67; setLocation 716 114; 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; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; showCharacters #8835592963818847919 #mesquite.lists.CharacterList.CharacterList; tell It; setData 0; getWindow; tell It; newAssistant #mesquite.lists.CharListInclusion.CharListInclusion; newAssistant #mesquite.stochchar.CharListProbModels.CharListProbModels; newAssistant #mesquite.lists.CharListCodonPos.CharListCodonPos; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -67; setLocation 716 114; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; endTell; showWindow; getEmployee #mesquite.lists.CharListAnnotPanel.CharListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; endTell; end;