#NEXUS [written Thu Jul 17 17:33:34 JST 2014 by Mesquite version 2.75 (build 564) at Glaucophyceae/133.11.3.85] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=6; TAXLABELS 'Cyanophora paradoxa CCAP 981/1' 'Cyanophora kugrensii NIES-763' Cyanophora_cuspidata_SAG_45.84 Cyanophora_cuspidata_101 Cyanophora_biloba_UTEX_2766 'Cyanophora sudae NIES-764' ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=614; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX 'Cyanophora paradoxa CCAP 981/1' ACACTGTATCCAATATACCTTGTGAACTGTTCTGTTCGGGTGCCAGGTTGTCGGCGCTCGCATACCTTC-TGGTATGCTTGTTTCCGATGCCTGGTGCCGTATCACTTTAAACCCATTTCATACCTTTGACTGAATCTATGCTAGTGACGCAAGTCCTGGCAA-TCTTAATAAAAAACAACTTTTAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCAAATCTTTGAACGCATATTGCGCTTCTGGGCTCGCTCAGAAGCATGTCTGTTTCAGTGTCATTATCATCATCCTCACCATACCTTTATGGTCCCTGGTGGACTTGAGCGTCATAGGGTCTTCGGAACCTATGTTGCTTGAAATTCAGAGGTTACTGGGACGGTAGCTGTCCTAAGTGGTGTATTAATCTGCCTCGGCAGAAAATCACC-TCTTAGTAAGCTGCCCTCGTTGTGCTCAGTTTCCACCTGCTT-GCATTTTTAATTTTGACCTGAAATCAGGCAAGGCCACCCGCTGAACTTAAGCATATTAATAAGCGGAGGAAAAGAAACTAACAAGGATTCC 'Cyanophora kugrensii NIES-763' ACACTGTATCCAATATACCTTGTGAACTGTTCTGTTTGGGTGCCAGGTTGTCGGCGCTCGCATACCTTTATGGTATGCTTGTTTCCGCT-CCTGGTGCCGTATCACTTTAAACCCATTTCATACCTTTGACTGAATCTATGCTAGTGACGCAAGTCCTGGCAA-TCTTAATAAAAAACAACTTTTAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCAAATCTTTGAACGCATATTGCGCTTCTGGGCTCGCTCAGAAGCATGTCTGTTTCAGTGTCATTATTATCATCCTCACCATACCTTTATGGTCCCTGGTGGACTTGAGCTTCATAGAATCTTCGGAAGCTATGTTGCTTGAAATATAGAGGTTACTGGGACGGTAGCTGTCCTAAGTGGTGTATTAATCTGCTTCGGCAGAAAATCACC-TCTTAGTAAGCTGCCCTCGTTGTGCTCAGTTTCCACCTGCTT-GCATTTTTAATTTTGACCTGAAATCAGGCAAGGCCACCCGCTGAACTTAAGCATATTAATAAGCGGAGGAAAAGAAACTAACAAGGATTCC Cyanophora_cuspidata_SAG_45.84 ACACTGTATCCAATATACCTTGTGAACTGTTCTGTTTGGGTGCCAGGTTGTCGGCGCTCGCATACCTTTATGGTGTGCTTGTTTCCGCT-CCTGGTGCCGTATCACTTTCAACCCATTTCATACCTTTGACTGAATCTATGCTAGTGACGCAAGTCCTGGCAA-TCTTAATAAAAAACAACTTTTAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCAAATCTTTGAACGCATATTGCGCTTCTGGGCTCGCTCAGAAGCATGCCTGTTTCAGTGTCATTATTATCATCCTCATCATACCTTTATGGTC--TGATGGACTTGAGCTTCATAGAATCTTCGGAAGCTATGTTGCTTGAAATTCAGAGGTTACTGGGACGGTAGCTGTCCTAAGTGGTGTATTAATCTGCTTCGGCAGAAAATCACC-TCTTAGTAAGCTGCCCTCGTTGTGCTCAGTTTCCACCTGCTTAGCATCTTTAATTTTGACCTGAAATCAGACAAGGCCACCCGCTGAACTTAAGCATATTAATAAGCGGAGGAAAAGAAACTAACAAGGATTCC Cyanophora_cuspidata_101 ACACTGTATCCAATATACCTTGTGAACTGTTCTGTTTGGGTGCCAGGTTGTCGGCGCTCGCATACCTTTATGGTGTGCTTGTTTCCGCT-CCTGGTGCCGTATCACTTTCAACCCATTTCATACCTTTGACTGAATCTATGCTAGTGACGCAAGTCCTGGCAA-TCTTAATAAAAAACAACTTTTAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCAAATCTTTGAACGCATATTGCGCTTCTGGGCTCGCTCAGAAGCATGTCTGTTTCAGTGTCATTATTATCATCCTCATCATACCTTTATGGTC--TGATGGACTTGAGCTTCATAGAATCTTCGGAAGCTATGTTGCTTGAAATTCAGAGGTTACTGGGACGGTAGCTGTCCTAAGTGGTGTATTAATCTGCTTCGGCAGAAAATCACC-TCTTAGTAAGCTGCCCTCGTTGTGCTCAGTTTCCACCTGCTTAGCATCTTTAATTTTGACCTGAAATCAGGCAAGGCCACCCGCTGAACTTAAGCATATTAATAAGCGGAGGAAAAGAAACTAACAAGGATTCC Cyanophora_biloba_UTEX_2766 ACACTGTATCCAATATACCTTGTGAACTGTTCTGTTCGGGTGCCTGGTTGTCGGCGCTCGCATACCTTTACGGTGTGCTTGCGTCCACAGCCTGGTGCCGTATCACTTTACACCCATTTCATACCTTTGACTGAATCTCTGCTAGTGACGCAAGTCCTGGCAAATCT-AATAAAAAACAACTTTTAACAACGGATATCTTGGTTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCAAATCTTTGAACGCATATTGCGCTTCTGGGCTCGCTCAGAAGCATGTCTGTTTCAGTGTCATTATCATCATCCTCACCATACCTTTATGGTCCCTGGTGGACTTGAGTTTCATAGCATTTTCGGATGCTATGTTACTTGAAATATAGAGGTTACTGGGACGGTGGCTGTCCTAAGTGGTGTATTAATCTGCTTCGGCAGAAAATCACCATTTTAGTATGCTGCCCTCGTTGTGCTCAGTTTCCACCTGCTT-GCATTTTTAATTTTGACCTGAAATCAGGCAAGGCCACCCGCTGAACTTAAGCATATTAATAAGCGGAGGAAAAGAAACTAACAAGGATTCC 'Cyanophora sudae NIES-764' ACACTGTATCCAATATACCTTGTGAACCGTTCTGTTCGGGTGCCAG-TTGTCGGCGCTCGCATACCTTTATGGTATGCTTGTTTCCGACGACTGGTGCCGTATCACTTCACACCCATTTCATACCTTTGACTGAATCTCTGCTAGTGACGCAAGTCCTGGCAAATCT-AATTAAAAACAACTTTTAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCAAATCTTTGAACGCATATTGCGCTTCTGGGCTCGCTCAGAAGCATGTCTGTTTCAGTGTCATTATCATCATCCTCACCATACCTTTATGGTCCCTGGTGGACTTGAGCTTCATAGCGTCTTCGGATGCTATGTTGCTTGAAATATAGAGGTTACTGGGACGGTAGCTGTCCTAAGTGGTGTATTAATCTGCTTCGGCAGAAAATCACCATCTTAGTAAGCTGCCCTCGTTGTGCTCAGTTTCCACCTGCTT-GCATTTTTAATTTTGACCTGAAATCAGGCAAGGCCACCCGCTGAACTTAAGCATATTAATAAGCGGAGGAAAAGAAACTAACAAGGATTCC ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 614; END; BEGIN TREES; Title Imported_trees; LINK Taxa = Taxa; TRANSLATE 1 'Cyanophora paradoxa CCAP 981/1', 2 'Cyanophora kugrensii NIES-763', 3 Cyanophora_cuspidata_SAG_45.84, 4 Cyanophora_cuspidata_101, 5 Cyanophora_biloba_UTEX_2766, 6 'Cyanophora sudae NIES-764'; TREE Imported_tree_0 = ((((4:0.0,3:0.00332992)0.9980:0.01182509,2:0.0)0.5520:0.00590818,1:0.01290008)0.8460:0.00617415,(6:0.00910018,5:0.02591717)0.8460:0.00132017); END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 614; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 614; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1405586015051; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 1581081123667798065; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 2107891556341420610; mqVersion 275; checksumv 0 3 3283957036 null getNumChars 614 numChars 614 getNumTaxa 6 numTaxa 6 short true bits 15 states 15 sumSquaresStatesOnly 87715.0 sumSquares 87715.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1 errorReportedDuringRun; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1366 659; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #1581081123667798065 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1356.1405585922120.1549782208288070056; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1266 592; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; 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 #2107891556341420610 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 279; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1266 592; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; 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; getWindow; tell It; forceAutosize; endTell; hideWindow; 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;