#NEXUS [written Thu Jul 09 11:27:30 CST 2015 by Mesquite version 3.03 (build 702) at Yu-2015/192.168.1.164] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=11; TAXLABELS Potamogeton_distinctus_YI1686 Althenia_filiformis_YI1977 Althenia_orientalis_YI1562 Lepilaena_australis_YI1917 Lepilaena_bilocularis_YI1918 Lepilaena_cylindrocarpa_YI1106 Lepilaena_preissii_YI1082 Pseudalthenia_aschersoniana_YI1981 Zannichellia_obtusifolia_YI1542 Zannichellia_palustris_YI1473 Zannichellia_peltata_YI1470 ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=663; FORMAT DATATYPE = DNA INTERLEAVE GAP = - MISSING = -; MATRIX Potamogeton_distinctus_YI1686 AATGTCAATGACGCAGGGTCTGATCAGCAATCAAAGGGTAGGAAGCTCTGGGGTTTGGTAGTTTGCCATCACACAACTCCAAAGTTTGTCCCCTTTCCTCTTAGGTATGCTTGTGAATTTCTGCTTCAAGTTTTTGGTATACAATTGAACAAGGAGGTGGAATTGTCTGCTCAAACAAGGGAGAAAGATATACTAAAGACACAAGCTGTTCTTTGCGACATGCTTCTCAGAGATCCGCCCGTGGGGATATTCACTCAAACTCCTAATATTATGGATCTGGTGAAGTGTGATGGTGCTGCTCTATATTATAGAAACCAGTTTTGGCTACTTGGAGTAACACCCACTAGGGTACAGATAAAAGAGATAGCTAGATGGCTTCTGGAGTGTCATGATGGCACTACTGGATTAAGTACGGATAGCATTTCAGAGGCAGGTTGTCCAGGTGCACAAGTGCTAGGAGATGCTGTCTGTGGTATGGCTGCTATCAAAATCACCAACAAGGACTTTATTTTCTGGTTTCGATCCCACACAGCAAAAGATATTAAATGGGGAGGAGCTAAAAATGATCCAACTGATATGAACATTGATAGCACGCAGATGCACCCACGTTCTTCATTCAACGCTTTCTTGGAAGTTGTCAAGCAACGGAGTCTTCCATGGGAA Althenia_filiformis_YI1977 TGTGTGAATAACACGAGTTCTGATCAACAAGCGAAGGGTAGGAAGCTCTGGGGTTTGGTAGTTTGCCATAATGCAACTCCAAGATTCATCCCGTTTCCTCTTAGGTATGCTTGTGAATTTCTGCTTCAAGTTTTTGCTATACAACTTAACAAGGAGGTGGAATTGGCTAGTCAAACAAGGGAGAAAAATATAATAAAAACACAAGCTTTTCTTTGCGACATGCTTCTCAGAGACTCGCCTGTAGGGATATTTACTCAAACTCCTAATGTTATGGATCTAGTGAAGTGTGATGGTGCTGCCCTATATTATAGAAACCAATTTTGGTTACTTGGTATAACACCTACTAAGATTCAGATAAAAGAGATGACCAGGTGGCTTCTGGAATATCATAATGGCACTACCGGAATAAGTACAGATAGCATTTCAGAGGCAGGTTGTCCAGGTGCACAGGTGCTGGGAGATGCTGTTTGTGGTATGGCTGCTGTCAAAATCACTGATAAGGACTTTATTTACTGGTTTCGATCACACACAGCAAAAGAGATTAAATGGGGAGGAGCTAAAAATGATCCAACTGATATGGACACTGATAACACACAGATGCACCCACGTTCTTCATTCAACGCTTTCCTAGAAGTCATCAAGCAAAGGAGTCTTCCATGGGAA Althenia_orientalis_YI1562 TGTGTGAATAACACGAGTTCTGATCAACAAGCGAAGGGTAGGAAGCTCTGGGGTTTGGTAGTTTGCCATAATGCAACTCCAAGATTCATCCCCTTTCCTCTTAGGTATGCTTGTGAATTTCTGCTTCAAGTTTTTGCTATACCACTTAACAAGGAGGTGGAATTGGCTAGTCAAACAAGGGAGAAAAATATAATAAAAACACAAGATTTTCTTTGCGACATGCTTATCAGAGACTCGCCTGTAGGGATATTTACTCAAACTCCTAATGTTATGGATTTAGTGAAGTGTGATGGTGCTGCCCTATATTATAGAAACCAATTTTGGTTACTTGGTATAACACCTAATAAGATTCAGATAAAAGAGATGACCAGGTGGCTTCTGGAATATCATAATGGCACTACCGGAATAAGTACAGATAGCATTTCAGAGGCAGGTTGTCCAGGTGCACAGGTGCTGGGAGATGCTGTTTGTGGTATGGCTGCTGTCAAAATCACTGATAAGGACTTTATTTACTGGTTTCGATCACACACAGCAAAAGAGATTAAATGGGGAGGAGCTAAAAATGATCCAACTGATATGGACACTGATAACACACAGATGCACCCACGTTCTTCATTCAACGCTTTCCTAGAA------------------------------ Lepilaena_australis_YI1917 TGTGTGAATAACTTGAGTTCTGAGCAACAGGCAAAGGGTAGGAAGCTCTGGGGTTTGGTAGTTTGCCATCATGCAACTCCGAGATTTATTCCATTTCCTCTTAGGTATGCTTGTGAATTTCTGCTTCAAGTTTTTGGTATACAACTGAACAAGGAGGTGGAACTTGCTGCTCAAACAAGGGAGAAAAATATAATAAAAACACAAGCTTTTCTTTGCGATGTGCTTCTTAGAGATTCACCTGTGGGGATATTTACTCAAACTCCTAACGTTATGGATCTAGTGAAGTGTGATGGTGCTGCCTTATATTATAGAAACCAGTTTTGGTTACTTGGGATAACACCTACTAAGATGCAGATAAAAGAGATGGCCAGATGGCTTCTGGAATGTCATAATGGCACAACCGGTTTAAGTACAGATAGCATTTCAGAGGCAGGTTGTCCAGGTGCACAAGTGCTGGGAGATGCTGTCTGTGGTATGGCTGCTGTCAAAATCACTGACAAGGACTTTATTTTCTGGTTTCGATCCCACACAGCAAAAGAAATCAAATGGGGAGGAGCTAAAAATGATCCAACTGATATGAACATTGATAGCACACAGATGCATCCACGTTCTTCATTCAATGCTTTCCTAGAAGTTGTCAAGCAAAGGAGCCTTCCATGGGAG Lepilaena_bilocularis_YI1918 TGTGTGAATAACGCGAGTTCTGAACAACAAACAAAGGGTAGGAAGCTCTGGGGTTTGGTAGTTTGCCATCATGCAACTCCGAGATTTATCCCATTTCCTCTTAGGTATGCTTGTGAATTTCTGCTTCAAGTTTTTGGTATACAACTGAACAAGGAGGTGGAGTTGGCTGCTCAAACAAGGGAGAAAAATATAATAAAAACACAAGCTTTTCTTTGCGACGTGCTTCTCAGAGACTCACCTGTAGGGATATTTACTCAAACTCCTAATGTTATGGATCTAGTGAAGTGTGATGGTGCTGCCCTATATTATAGAAACCAATTTTGGTTACTTGGGATAACACCTACTAAGATGCAGATAAAAGAGATGGCCAGATGGCTTCTGGAATGTCATAATGGCACTACTGGATTAAGTACAGATAGCATTTCAGAGGCAGGTTGTCCAGGTGCACAAGTGCTGGGAGATGCTGTCTGTGGTATGGCTGCTGTCAAAATAACTGACAAGGACTTTATTTTCTGGTTTCGATCCCACACAGCAAAGGAGGTTAAATGGGGAGGAGCTAAAAATGATCCAACTGATATGAACATTGATAGCACACAGATGCACCCACGTTCTTCATTCAATGCTTTCCTAGAAGTTGTCAAGCAAAGGAGCCTACCATGGGAA Lepilaena_cylindrocarpa_YI1106 TGTGTGAATAAAACGAGTTCCGATCAACAAGCGAAGGGTAGGAAGCTCTGGGGTTTGGTAGTTTGCCATAATGCAACTCCGAGATTTATCCCGTTTCCTCTTAGGTATGCTTGTGAGTTTCTGCTTCAAGTTTTTGGTATACAACTGAACAAGGAGGTGGAATTGGCTACTCAAACAAGGGAGAAAAATATAATAAAAACACAAGCTTTTCTTTGCGACATGCTTCTCAGAGACTCKCCTGTAGGGATATTTACTCAAACTCCTAATGTTATGGATCTAGTRAAGTGTGATGGTGCTGCCCTATATTATAGAAACCAATTTTGGTTACTTGGTATAACACCTACTAARATGCAGATAAAAGAKATGWCCAACTGGCTTYTGGAATAYCATAATGGSACTACCGGATTAAGTACMGATAGCCTTTCRGAGGCCGGTTGTCCAGGTGCACAAGTGCTGGGAGATGCTGTMTGYGGTATGGCTGCTGTCAAAATCACTGACAAGGACTTTATTTTCTGGTTTCGATCCCAYACAGCAAAAGAAATTAARTGGGGAGGAGCTAAAAATGATCCAAATGATATGAACACTGATRGCACACAGATGCAYCCGCGTTCTTCATTCAATGCTTTYCTAGAGGTTGTCATGCAAAGGAGCCTTCCATGGGAA Lepilaena_preissii_YI1082 TGTGTGAATAACACGAGTTTTGATCAACAAGCGAAGGGTAGGAAGCTGTGGGGTTTGGTAGTTTGCCATAATGCAAATCCGAGATTTATCCCGTTTCCACTTAGGTATGCTTGTGAACTTCTGCTTCAAGTTTTTGGTATTCAACTGAACAAAGAGGTGGAATTGACTACTCAAAAAAGGGAGAAAAATATAATAAAAACACAAGCTTTTCTTTGCGACATGCTTCTCAGAGACTCACCTGTAGGGATATTTACTCAAACTCTTAATGTTATGGTTCTAGTGAAGTTTGATGGTGCTGCCCTATATTATAGAAACCAATTTTGGTTATTTGGTATAACACCTACTAAGATGCAGATAAAAGAGTTGACCAGGTGGCTTCTGGAATATCATAATGGCACTACCGGATTAAGTACTGATAGCATTTCAGAGGCAGGTTGTCCAGGTGCACAAGTGTTGGGAGATGTTGTCTGTGGTATGGCTGCTGTCAGAATCACCGACAAGGACTTTATTTTCTGGTTTCGATCCCACACAGCAAAAGAGATTAAATGGGGAGGAGCTAAAAATGATCCAACTGATATAAACACTGATAGCACACAGATGCATCCACGTTCTTCATTCAAGACTTTCCTAGAGGTTGTCAAGCAAAGGAGCCTTCCATGGGAA Pseudalthenia_aschersoniana_YI1981 AATGTGAATGAGGCAGGGTCTGATCAACAACCAAAGGGTAGGAAGCTCTGGGGTTTGGTAGTCTGCCATCATTCAACTCCAAGGTTTGTCCCCTTTCCTCTTAGATATGCTTGTGAATTTCTGCTTCAAGTTTTTGGTATACAACTAAACAAGGAAGTGGAATTGGCTGCTCAAACAAGGGAGAAAAATATAATAAAGACGCAAGCTTTTCTTTGCGACGTACTTCTCAGAGATTCACCTGTAGGGATATTTACTCAAACTCCAAATGTTATGGATCTAGTAAAGTGTGATGGTGCTGCACTATATTTTAGAAACGAGTTTTGGTTGCTTGGGGTAACACCTACTAGGATACAAATAAAAGAGATGGCTAGATGGCTTCTGGAGTATCATGATGGCACCACTGGATTAAGTACGGATAGCATTTCAGAGGCAGGTTGTCCAGGTGCACAAGTTCTGGGAGATGCTGTCTGTGGTATGTCTGCTATCAAGATTACCAACAAGGACTTTATTTTCTGGTTTCGATCGCACACAGAAAAAGAAATTAAATGGGGAGGAGCTAAAAATGATCCAACAGATGTGAATACTGATAGCACACAAATGCATCCACGTTCTTCATTCAATGCTTTCCTGGAAGTTGTCAAGCAAAGGAGTCTTCCATGGGAA Zannichellia_obtusifolia_YI1542 AATGAGAATGAGGCAGGGTCTGATCAACAACCAAAGGGTAGGAAGCTCTGGGGTTTGGTAGTTTGCCATCATTCAACTCCGAGGTTTGTCCCCTTTCCCCTTAGGTATGCTTGTGAATTTCTTCTTCAAGTTTTTGGTATACAACTGAACAAGGAAGTAGAATTGGCTGCTCAAACAAGGGAGAAAAATATAATAAAGACACAAGCTTTTCTTTGTGACGTGCTTCTCAGAGATTCACCTGTAGGAATATTTACTCAAACTCCAAACGTTATGGATCTAGTCAAATGTGATGGTGCTGCACTATATTATAGAAATGAGTTTTGGTTACTTGGGGTAACACCCACTAGGATGCAAATAAAAGAGATGGCTAGATGGCTTCTGGAGTATCATGATGGCACCACTGGATTAAGTACGGATAGCATTTCAGAGGCGGGTTGTCCAGGTGCACAAGCGCTGGGAGATGCAGTCTGTGGTATGGCTGCTATCAAAATTACCAACAAGGACTTTATTTTCTGGTTTCGATCCCACACAGCGAAAGAAATTAAATGGGGAGGAGCTAAAAATGATCCAACTGATATGAATACTGATAGCACACAAATGCATCCACGTTCTTCATTCAATGCTTTCCTAGAAGTTGTCAAGCAAAGGAGTCTTCCATGGGAA Zannichellia_palustris_YI1473 AATGAKAAKGWGGCAGGGTCTGATCAACAACCAAAGGGTAGGAAGCTMTGGGGTTTGGTAGTTTGCCATCATTCAACTCCGARGTTTGTCCCCTTTCCTCTTAGGTATGCTTGTGAATTTCTKCTTCAAGTTTTTGGTATACAACTSAACAAGGAAGTRGAATTGGCTGCTCAAACAAGGGAGAAAAATATAATAAAGACACAAGCTTTTCTTTGYGACGTACTTCTCAGAGATTCACCTGTAGGGATATTTACTCAAACTCCAAACRTTATGGATCTAGTAAARTGTGATGGTGCTGCACTATATTATAGAAAYGAGTTTTGGTTACTTGGGGTAACACCYACYAGGATRCAAATAAAAGAGATGGCTAGATGGCTTCTGGAGTATCATGAYGGCACCACTGGATTAAGTACRGATAGCATTTCAGAGGCAGGTTGTCCAGGTGCRCAAGYGCTGGGARATGYWGTCTGTGGTWTGGCTGCTATCAAAATTACCAACAAGGACTTTATYTTYTGGTTTCGATCCCACACAGCAAAAGAAATTAAATGGGGAGGAGCTAAAAATGATCCAACTGATATGAATACTGATAGCACACARATGCATCCACGYTCTTCATTCAATGCTTTCCTRGAAGTTGTCAAGC-------------------- Zannichellia_peltata_YI1470 AACGAGAATGAGGCAGGGTCTGATCAACCACCAAAGGGTAGGAAGCTCTGGGGTTTGGTAGTTTGCCATCATTCAACTCCGAGGTTTGTCCCCTTTCCTCTTAGGTATGCTTGTGAATTTCTTCTTCAAGTTTTTGGTATACAACTGAACAAGGAAGTAGAATTAGCTGCTCAAACAAGGGAGAAAAATATAATAAAGACACAAGCTTTTCTTTGCGACGTACTTCTCAGAGATTCACCTGTAGGGATATTTACTCAAACTCCAAACGTTATGGATCTAGTAAAATGTGATGGTGCTGCACTATATTATAGAAACGAGTTTTGGTTACTTGGGGTAACACCCACTAGGATGCAAATAAAAGAGATGGCTAGATGGCTTCTGGAGTATCATGATGGCACCACTGGATTAAGTACGGATAGCATTTCAGAGGCAGGTTGTCCAGGTGCACAAGCGCTGGGAGATGCAGTCTGTGGTATGGCTGCTATCAAAATTACCAACAAGGACTTTATTTTCTGGTTTCGATCCCACACAGCAAAAGAAATTAAATGGGGAGGAGCTAAAAATGATCCAACTGATATGAATACTGACAGCACACAAATGCATCCACGTTCTTCATTCAATGCTTTCCTAGAAGTTGTCAAGCAAAGGAGTCTTCCATGGGAA ; END; begin paup; set autoclose = yes warnreset = no increase = prompt; set criterion = parsimony; hsearch; pset opt = acctran; roottrees outroot = monophyl; describetrees all / plot = phylogram brlens = yes; savetrees file = Najas_rbcL.tre brlens = yes; contree all / strict = yes tcompress = yes treefile = NrbcLcontree.tre; bootstrap nrep = 1000 treefile = NrbcLbs.tre; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 663; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 663; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 663; END; BEGIN TREES; Title 'Trees from "Zannichellia_phyC.MP.contree...tre"'; LINK Taxa = Taxa; TRANSLATE [0] 1 Potamogeton_distinctus_YI1686, [1] 2 Althenia_filiformis_YI1977, [2] 3 Althenia_orientalis_YI1562, [3] 4 Lepilaena_australis_YI1917, [4] 5 Lepilaena_bilocularis_YI1918, [5] 6 Lepilaena_cylindrocarpa_YI1106, [6] 7 Lepilaena_preissii_YI1082, [7] 8 Pseudalthenia_aschersoniana_YI1981, [8] 9 Zannichellia_obtusifolia_YI1542, [9] 10 Zannichellia_palustris_YI1473, [10] 11 Zannichellia_peltata_YI1470; TREE Strict = (1,(((((2,3)100,6,7)99,5)84,4)100,(8,(9,10,11)94)99)); END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1436412450881; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 7117831968280414897; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 601894461268199798; mqVersion 303; checksumv 0 3 3210559708 null getNumChars 663 numChars 663 getNumTaxa 11 numTaxa 11 short true bits 2305843009213693967 states 15 sumSquaresStatesOnly 167627.0 sumSquares -9.223372036854773E19 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.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #7117831968280414897 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1411.1436412430616.8472232608622995613; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 600 392; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareLineTree.SquareLineTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; setFixedTaxonDistance 0; endTell; setEdgeWidth 4; showEdgeLines on; orientUp; 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 off; toggleColorAssigned 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 off; 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 #601894461268199798 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 600 392; setLocation 8 8; 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; toggleShowPaleExcluded 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;