#NEXUS [written Mon Oct 28 16:54:34 CET 2019 by Mesquite version 3.40 (build 877) at mdk-crou-006.cbs-niob.local/10.136.73.120] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=4; TAXLABELS Delitschia_confertaspora_MF459003.1 Fusculina_eucalyptorum_CBS_145083 Fusculina_eucalypti_CBS_120083 Fusculina_regnans_CPC_32732 ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=770; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Delitschia_confertaspora_MF459003.1 ----------------------------------------gcgcacgaggtcaagatgcggcggcgcttgcgccgctcaatccgccgccaggggctttaaaaccccccccggcggcggaacctcagccaggtcgaacccatccggtttggcgtggccagctgcgtggcagccagccttacacacccgtgaggt-acattttccgcaacgc-----tgttgggccgtggcccgcaacacgtataaacccttctatccttgactatgagcacccatgtttcctcggcgggctcgcccgccggtggaccccttcaaaaccacttttgcatcataacgcgtgttgtctgagcgatacaagcaaatcttattaaaactttcaacaacggatctcttggttctggcatcgatgaagaacgcagcgaaatgcgataagtagtgtgaattgcagaattcagtgaatcatcgaatctttgaacgcacattgcgccctttggcattcccgaagggcatacctgttcgagcgtcatcgcactaatcaagctctgcttggtgttgggcgcttgtcccgcgattc---tgcgcggactcgcctcaaaagcatcggcgttggcatgcgtgggcctcgagcctaccaaaccattcgcgacgtaggcccccgtggcagcagccgcaacaaacttttcctcag----tttgacctcggatcaggtagggatacccgctgaacttaagcatatcaataagcggaggaaaagaaaccaaccagggattg Fusculina_eucalyptorum_CBS_145083 ----------gtaggtgaacctgcggaaggatcattatatatctgagtggatcaggtgctcaattctaatgcaggcgtgttctcttgggaatgatggcccgcact-gcctgtgaaggagggttc-acccctcccagcaggctgtgttctcccctcgtaagaggggggctacacggcgttcgctgtgatgagggtttagaatcctagagacccctgcgttaagtatttggtgctgcgtctt-ctcaccttaccaccacccttcatgagtacttgtgtttccttggccggtccgccggccactggaccttcagtaaccaaatgtaatact------tgatttgtctgaatcaaagca--aaattaaattaaaactttcaacaatggatctcttggctctggcatcgatgaagaacgcagcgaaatgcgataagtagtgtgaattgcagatctccgtgaatcatcgaatttttgaacgcacattgcgccctttggaattcct-tagggcatgcctgttcgagcgtcgtttcaatgttcaagctttgcttggtgttgggcgcctgtccccgccttcttgcgtagggactcgccttaaatctatcagcgtctgcatggttaggctaagagcgcagcagatta--cagcgcctcaaagcctggtgtagcacctgctgtaaaactatcattttaacttttgacctcgaatcaggtagggatacccgctgaacttaag---------------------------------------- Fusculina_eucalypti_CBS_120083 ---ggtttccgtaggtgaacctgcggaaggatcattatacatctgagtagattaggtgcttaggtgcttaatgtggttgctttgtcaggaatgataacctgcaccagcttgcaaaggggggctcttcccctccgagcaggctgtgttcccccttcgtaagaggggggctacgcggcgctcgccgtgatgaagg-ttagaatcctagaggcctctatgtttagtatctggtgctgtgtcttactcaccttaccaccacccttcatgagtacttgtgtttccttggccggtccgctggccactggaccttcagtaaccaaatgtaatact------tgaattgtctgaatcaaatcaa-aaattaaattaaaactttcaacaatggatctcttggctctggcatcgatgaagaacgcagcgaaatgcgataagtagtgtgaattgcagatctccgtgaatcatcgaatttttgaacgcacattgcgccctttggaattcct-tagggcatgcctgttcgagcgtcgtttcaatgttcaagctttgcttggtgttgggcgtctgtccctgccttcatgtgtggggactcgccttaaatctatcagcgtctgcagggttaggctacgagcgcagcagatta--cagcgcctcaaagcctggcgtagcacccgctgtaaaactatcatttaaacttttgacctcgaatcaggtagggatacccgctgaacttaagcatatcaataagcggaggaaaagaaaccaa-cagggattg Fusculina_regnans_CPC_32732 acaaggtttcgtaggtgaacgtgcggaaggatcattatatatctgagtagattaggtgcttcggtgctttatgtgggtgctttctcaggaatgataacctgcaccagcctgcaaagagggggttcccccctccaagcaggctgtgttcccccttcgtaagaggggggctacgcggtgctcgccgtgatgaggg-ttagaatcctagaggcctctgtatttagtatctggtgctgtgtcttactcaccttaccaccacccttcatgagtacctgtgtttccttggctggtctgccagccactggaccttcagtaaccaaatgtaatact------tgaattgtctgaatcaaagcaa-aaattaaattaaaactttcaacaatggatctcttggctctggcatcgatgaagaacgcagcgaaatgcgataagtagtgtgaattgcagatctccgtgaatcatcgaatttttgaacgcacattgcgccctttggaattcct-tagggcatgcctgttcgagcgtcgtttcaatgttcaagctttgcttggtgttgggcgtctgtccccccgttcatgtgtggggactcgccttaaatctatcagcgtctgcagggttaggctacgagcgcagcagatta--cagcgcctcaaagcctggcgtagcacccgctgtaaaactatcatttaaacttttgacctcgaatcaggtagggatacccgctgaacttaagcatatc---------------------------------- ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 770; END; BEGIN PAUP; LOG start = yes append = yes; set autoclose = yes warnreset = no torder = right; OUTGROUP outgroups / only; exclude 1 - . / only; include combined / only; SET CRITERION = parsimony maxtrees = 1000 increase = no storebrlens = yes outroot = paraphyl; Pset gapmode = newstate; HSEARCH ADDSEQ = random NREPS = 100 SWAP = TBR; roottrees ROOT = OUTGROUP OUTROOT = MONOPHYL; Savetrees format = nexus brlens = yes maxdecimals = 0 file = FusculinaITSparsimony.trees; PSCORES 1 / TL = yes CI = yes RI = yes RC = yes HI = yes; Contree ALL / strict = yes treefile = FusculinaITSparsimonycons.tre; Bootstrap nreps = 1000 search = heuristic; Savetrees from = 1 to = 1 format = nexus brlens = yes savebootp = nodelabels maxdecimals = 0 file = FusculinaITSparsimonybootstrap.tre; Log stop = yes; END; BEGIN SETS; CHARSET combined = 41 - 730; TAXSET outgroups = 1; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 770; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 770; END; BEGIN TREES; Title 'Trees from "Fig 40.trees"'; ID 016e1312564f1; LINK Taxa = Taxa; TRANSLATE [0] 1 Delitschia_confertaspora_MF459003.1, [1] 2 Fusculina_eucalyptorum_CBS_145083, [2] 3 Fusculina_eucalypti_CBS_120083, [3] 4 Fusculina_regnans_CPC_32732; TREE Fig._40 = (((3:11,4:13):19,2:35):144,1:117):0.0; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1572278074852; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 9122030578940609927; tell It; setDefaultOrder 3 2 0 1; attachments ; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 2170057796549996083; mqVersion 340; checksumv 0 3 2495173571 null getNumChars 770 numChars 770 getNumTaxa 4 numTaxa 4 short true bits 1152921504606846991 states 15 sumSquaresStatesOnly 64358.0 sumSquares -1.8123926052419634E21 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 609; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 2555 1458; setLocation 340 23; setFont SanSerif; setFontSize 18; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #9122030578940609927 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; setTreeBlockID 016e1312564f1; toggleUseWeights off; endTell; setAssignedID 996.1572278002038.969403818768858015; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1946 1386; setLocation 340 23; setFont SanSerif; setFontSize 18; getToolPalette; tell It; 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 off; toggleEven off; setFixedTaxonDistance 0; 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 off; toggleColorAssigned on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setTree '(1:117,(2:35,(3:11,4:13):19):144):0.0;'; 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; toggleShow consensusFrequency; toggleShow bootstrapFrequency; toggleShow posteriorProbability; toggleShow consensusFrequency; toggleShow posteriorProbability; toggleShow bootstrapFrequency; setDigits 4; setThreshold ?; 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 #2170057796549996083 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 862; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1946 1386; setLocation 340 23; setFont SanSerif; setFontSize 18; 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;