#NEXUS [written Fri Mar 02 16:20:55 CET 2018 by Mesquite version 3.10 (build 765) at Laia/161.116.70.234] BEGIN TAXA; DIMENSIONS NTAX=16; TAXLABELS Schmidtea_lugubris_MR00680_1 Schmidtea_lugubris_MR00680_2 Schmidtea_lugubris_lu7 Schmidtea_lugubris_lu5 Schmidtea_lugubris_lu4 Schmidtea_lugubris_lu6 Schmidtea_mediterranea_med1 Schmidtea_mediterranea_med2 Schmidtea_mediterranea_med01 Schmidtea_polychroa_p2 Schmidtea_polychroa_p3 Schmidtea_nova_MR00680_1 Schmidtea_nova_MR00680_4 Schmidtea_nova Schmidtea_nova_MR00680_2 Schmidtea_nova_MR00680_3 ; END; BEGIN CHARACTERS; DIMENSIONS NCHAR=321; FORMAT DATATYPE = DNA GAP = - MISSING = N; MATRIX Schmidtea_lugubris_MR00680_1 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAGTTAGCTATATATTATAGAGGTAAGGATTCTTCTTTTGGTCATTTGGGAATGATCTACGCTATGGTTAGAATTGGTTTCTTAGGTTTTTTAGTATGGGCACACCACATGTATACTGTTGGTTTGGATGTAGACTCTCGTGCTTATTTTACAGGTGCTACTATGATTGTTGGTGTACCTACTGGTATTAAGGTTTTTAGTTGGTTGGCAACTTTAAAAGGTTCTGAGTGATTTCTTTATTCTCAAAGTTTAGTAGTTGTTTTGTGAGTTTATGGTTTTATATTCTTG Schmidtea_lugubris_MR00680_2 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAGTTAGCTATATATTATAGAGGTAAGGATTCTTCTTTTGGTCATTTGGGAATGATCTACGCTATGGTTAGAATTGGTTTCTTAGGTTTTTTAGTATGGGCACACCACATGTATACTGTTGGTTTGGATGTAGACTCTCGTGCTTATTTTACAGGTGCTACTATGATTGTTGGTGTACCTACTGGTATTAAGGTTTTTAGTTGGTTGGCAACTTTAAAAGGTTCTGAGTGATTTCTTTATTCTCAAAGTTTAGTAGTTGTTTTGTGAGTTTATGGTTTTATATTCNNN Schmidtea_lugubris_lu7 ATACTCATTCTTCCAGGTTTTGGAATAATTTCACAGTTAGCTATATATTATAGAGGTAAGGATTCTTCTTTTGGTCATTTGGGAATGATCTACGCTATGGTTAGAATTGGTTTCTTAGGTTTTTTAGTATGGGCACACCACATGTATACTGTTGGCTTGGATGTAGACTCTCGTGCTTATTTTACAGGTGCTACTATGATTGTTGGTGTACCTACTGGTATTAAGGTTTTTAGTTGGTTGGCAACTTTAAAAGGTTCTGAGTGATTTCTTTATTCTCAAAGTTTAGTAGTTGTTTTGTGAGTTTATGGTTTTATATTCTTG Schmidtea_lugubris_lu5 ATTCTTATTCTTCCAGGTTTTGGAATAATTTCACAGTTAGCTATATATTATAGAGGTAAGGATTCTTCTTTTGGTCATTTGGGAATGATCTACGCTATGGTTAGAATTGGTTTTTTAGGTTTTTTAGTATGGGCACACCACATGTATACTGTTGGCTTGGATGTAGACTCTCGTGCTTATTTTACAGGTGCTACTATGATTGTTGGTGTACCTACTGGTATTAAGGTTTTTAGTTGGTTGGCAACTTTAAAAGGTTCTGAGTGATTTATTTATTCTCAAAGTTTAGTAGTTGTTTTGTGAGTTTATGGTTTTATATTCTTG Schmidtea_lugubris_lu4 ATACTTATTCTTCCAGGTTTTGGAATAATTTCACAGTTAGCTATATATTATAGAGGTAAGGATTCTTCTTTTGGTCATTTGGGAATGATCTACGCTATGGTTAGAATAGGTTTTTTAGGTTTTTTAGTATGGGCACACCATATGTATACTGTTGGCTTGGATGTAGACTCTCGTGCTTATTTTACAGGTGCTACTATGATTGTTGGTGTACCTACTGGTATTAAGGTTTTTAGTTGGTTGGCAACTTTAAAAGGTTCTGAGTGATTTATCTATTCTCAAAGTTTAGTAGTTGTTTTGTGAGTTTATGGTTTTATATTCTTG Schmidtea_lugubris_lu6 ATACTCATTCTTCCAGGTTTTGGAATAATTTCACAGTTGGCTATATATTATAGAGGTAAGGAGTCTTCTTTTGGTCACTTGGGAATGATCTACGCAATGGTTAGAATTGGTTTTTTAGGTTTTTTAGTATGGGCACACCACATGTATACTGTTGGCTTGGATGTAGACTCTCGTGCTTATTTTACAGGTGCTACTATGATTGTTGGTGTACCTACTGGTATTAAGGTCTTTAGTTGGTTGGCAACTTTAAAAGGTTCAGAGTGATTTATTTATTCTCAAAGTTTAGTAGTTGTTTTGTGAGTATATGGTTTCATATTCTTG Schmidtea_mediterranea_med1 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATTGGCTGTTTATTATAGTGGTAAGGAGGTTTCTTTTGGACATTTGGGTATGATTTATGCTATGATAAGAATTGGATTTTTAGGTTTCTTAGTTTGAGCTCATCATATGTATACTATAGGTTTAGATGTTGATTCTCGTGCTTATTTCACAGGAGCTACTATGATAGTTGGTGTTCCAACTGGAATAAAGGTATTTAGGTGGTTAGCTACTTTATATGGCTCTAATTGAGATTTGTACACACAGTGATCTGTTCCTGTATTATGGGTTTATGGGTTTATCTTCTTG Schmidtea_mediterranea_med2 ATTTTGATTCTTCCTGGGTTTGGTATTATTTCTCAATTGGCTGTTTATTATAGTGGTAAGGAGGTTTCTTTTGGACATTTGGGTATGATTTATGCTATGATAAGAATTGGATTTTTAGGTTTCTTAGTTTGAGCTCATCATATGTATACTATAGGTTTAGATGTTGATTCTCGTGCTTATTTCACAGGAGCTACTATGATAGTTGGTGTTCCAACTGGAATAAAGGTATTTAGGTGGTTAGCTACTTTATATGGCTCTAATTGAGATTTGTACACACAGTGATCTGTTCCTGTATTATGGGTTTATGGGTTTATCTTCTTG Schmidtea_mediterranea_med01 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATTGGCTGTTTACTATAGTGGTAAGGAGGTTTCTTTTGGGCATTTGGGTATGATTTATGCTATGATAAGAATTGGGTTTCTAGGTTTCTTAGTTTGAGCCCATCATATGTACACTATAGGTTTAGATGTTGATTCTCGAGCTTATTTCACAGGAGCTACTATGATAGTTGGTGTTCCCACTGGAATAAAGGTATTTAGGTGGTTAGCCACTTTATATGGTTCTAATTGAGATTTGTATACACAGTGATCCGTACCTGTGTTATGGGTTTATGGGTTTATTTTCTTG Schmidtea_polychroa_p2 ATTCTTATTCTTCCAGGGTTTGGCATTATTTCTCAATTGGCTATTTACTATAGAGGTAAGGATGCAGCTTTTGGACATTTGGGTATGATATATGCTATGGTAAGTATAGGTTTCTTGGGTTTCTTGGTTTGAGCTCATCATATGTATACTATAGGTTTAGATGTTGATTCTCGTGCTTACTTTACTGGGGCTACAATGATTGTTGGTGTTCCTACTGGTATTAAGGTATTTAGTTGATTAGCTACTTTGTACGGTTCTGAATGACGTTTATATTTTCATAGTGCAGTTTCTGTATTGTGGGTTTATGGGTTTATCTTTTTG Schmidtea_polychroa_p3 ATTCTTATTCTTCCAGGGTTTGGTATCATTTCTCAATTGGCTATTTATTATAGAGGTAAGGATGCAGCTTTTGGACATTTGGGTATGATATATGCTATGGTAAGTATAGGTTTCTTAGGTTTCTTAGTTTGAGCTCATCATATGTATACTATAGGTTTAGATGTTGATTCTCGTGCTTACTTTACTGGGGCTACAATGATTGTTGGTGTTCCTACTGGTATTAAGGTATTTAGTTGGTTAGCTACTTTGTACGGTTCTGAATGACGTTTATATCTTCATAGTGCAGTTTCTGTGTTGTGAGTTTATGGGTTCATCTTTTTG Schmidtea_nova_MR00680_1 ATTTTGATCTTACCTGGTTTTGGTATTATTTCTCAATTGGCTGTATATTACAGAGGTAAGGATGTTTCTTTTGGTCATTTAGGTATGATATATGCTATGGTTAGCATAGGCTTTTTAGGTTTTTTGGTTTGAGCACACCACATGTACACTGTTGGTTTAGATGTTGATTCTCGTGCTTATTTTACAGGTGCCACTATGATAGTTGGGGTTCCAACAGGTATAAAGGTGTTTAGTTGATTAGCAACTCTCTATGGTTCTGAGTGATACTTGTATGCACAAAGTGCTGTTGCTGTTTTGTGGGTTTATGGTTTTATTTTTCTT Schmidtea_nova_MR00680_4 ATTTTGATCTTACCTGGTTTTGGTATTATTTCTCAATTGGCTGTATATTACAGAGGTAAGGATGTTTCTTTTGGTCATTTAGGTATGATATATGCTATGGTTAGCATAGGCTTTTTAGGTTTTTTGGTTTGAGCACACCACATGTACACTGTTGGTTTAGATGTTGATTCTCGTGCTTATTTTACAGGTGCCACTATGATAGTTGGGGTTCCAACAGGTATAAAGGTGTTTAGTTGATTAGCAACTCTCTATGGTTCTGAGTGATACTTGTATGCACAAAGTGCTGTTGCTGTTTTGTGGGTTTATGGTTTTATTTTTCTT Schmidtea_nova ATTCTGATCTTACCTGGTTTTGGTATTATTTCTCAATTGGCTGTATATTACAGAGGTAAGGATGTTTCTTTTGGTCATTTAGGTATGATATATGCTATGGTTAGCATAGGCTTTTTAGGTTTTTTGGTTTGAGCACACCACATGTACACTGTTGGTTTAGATGTTGATTCTCGTGCTTATTTTACAGGTGCCACTATGATAGTTGGGGTTCCAACAGGTATAAAGGTGTTTAGTTGATTAGCAACTCTCTATGGTTCTGAGTGATACTTGTATGCACAAAGTGCTGTTGCTGTTTTGTGGGTTTATGGTTTTATTTTTCTT Schmidtea_nova_MR00680_2 ATTTTGATCTTACCTGGGTTTGGTATTATTTCTCAATTGGCTGTATATTACAGAGGTAAGGATGTTTCTTTTGGTCATTTAGGTATGATATATGCTATGGTTAGCATAGGCTTTTTAGGTTTTTTGGTTTGAGCACACCACATGTACACTGTTGGTTTAGATGTTGATTCTCGTGCTTATTTTACAGGTGCCACTATGATAGTTGGGGTTCCAACAGGTATAAAGGTGTTTAGTTGATTAGCAACTCTCTATGGTTCTGAGTGATACTTGTATGCACAAAGTGCTGTTGCTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Schmidtea_nova_MR00680_3 ATTTTGATCTTACCTGGGTTTGGTATTATTTCTCAATTGGCTGTATATTACAGAGGTAAGGATGTTTCTTTTGGTCATTTAGGTATGATATATGCTATGGTTAGCATAGGCTTTTTAGGTTTTTTGGTTTGAGCACACCACATGTACACTGTTGGTTTAGATGTTGATTCTCGTGCTTATTTTACAGGTGCCACTATGATAGTTGGGGTTCCAACAGGTATAAAGGTGTTTAGTTGATTAGCAACTCTCTATGGTTCTGAGTGATACTTGTATGCACAAAGTGCTGTTGCTGTTTTGTGGGTTTATGGTTTTATTTTTCTT ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 321; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 321; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 321; END; BEGIN TREES; Title Schmidtea_COI; ID 0161d588ab495; LINK Taxa = Taxa; TRANSLATE [0] 1 Schmidtea_lugubris_MR00680_1, [1] 2 Schmidtea_lugubris_MR00680_2, [2] 3 Schmidtea_lugubris_lu7, [3] 4 Schmidtea_lugubris_lu5, [4] 5 Schmidtea_lugubris_lu4, [5] 6 Schmidtea_lugubris_lu6, [6] 7 Schmidtea_mediterranea_med1, [7] 8 Schmidtea_mediterranea_med2, [8] 9 Schmidtea_mediterranea_med01, [9] 10 Schmidtea_polychroa_p2, [10] 11 Schmidtea_polychroa_p3, [11] 12 Schmidtea_nova_MR00680_1, [12] 13 Schmidtea_nova_MR00680_4, [13] 14 Schmidtea_nova, [14] 15 Schmidtea_nova_MR00680_2, [15] 16 Schmidtea_nova_MR00680_3; TREE 'PAUP_1' = (((10:0.030086,11:0.004373):0.133856,(9:0.061444,(7:0.0,8:0.0):0.0000000942125):0.17885):0.0718015,((14:0.0,((12:0.0,13:0.0):0.0,(15:0.0,16:0.0):0.003207):0.003183):0.138759,(6:0.027704,((4:0.003502,5:0.010196):0.003175,(3:0.0,(1:0.0,2:0.0):0.00369):0.006627):0.0000000480888):0.386618):0.0718015); END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1520004055142; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8265705871953779178; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 5730359036614544494; mqVersion 310; checksumv 0 3 2362341697 null getNumChars 321 numChars 321 getNumTaxa 16 numTaxa 16 short true bits 15 states 15 sumSquaresStatesOnly 159561.0 sumSquares 159561.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 214; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1600 781; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #8265705871953779178 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; setTreeBlockID 0161d588ab495; toggleUseWeights off; endTell; setAssignedID 1697.1520004011550.4168491942106447939; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1386 709; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; 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; togglePrintName on; 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; toggleShowOnTerminals 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; toggleShowOnTerminals on; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #5730359036614544494 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 216; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1386 709; 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.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.AlterData.AlterData; tell It; toggleBySubmenus off; 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 16 6 1 1; 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;