#NEXUS [written Mon Oct 28 17:23:03 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=6; TAXLABELS 'Melanconiella hyperopta NR_160258.1' Phaeothyriolum_dunnii_CPC_35847 Phaeothyriolum_eucalyptorum_HPC_2269 Phaeothyriolum_amygdalinum_CPC_36084 Phaeothyriolum_corymbiae_CPC_35789 Phaeothyriolum_corymbiae_MG386045.1 ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=740; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX 'Melanconiella hyperopta NR_160258.1' ------------------------------------------------------------------------AACAAGGTTTCCG----------------------------TTGGTGAACCAGCGGAGGGATCATTGATGGAACTTACGTCCCATATTACCCCTGTGAACTTATACC----TATATCGTTGCC-TCGGCGTAGGCCCGGGGGCCCTCTCCCCAGAGGGTCCCCCCACCGGTGGGAGCCCCACGGCTTCCCCCCTGTGGAGCAG-GCCCGTCGGCGGCCCCTATAAACCATTACTTGTAAAGAAGACCTTCTGAGTACAAACTTAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGCGAATTGCAGAATTCAGTGAGTCATCGAATCTTTGAACGCACATTGCGCC-------CGCTGGACATTCCGGCGGGCATGCCTGTTCGAGCGTCATTTC-ACCCCTCAGG----CTTCAGCGCCTGGTGTTGGGGCATAGCCTGTCAAAGGGCTAGCCCTCAAATTCAGTGGCGGAACCGCTG---GGACTCCGGGCGTAGTAATTTTTTCTCGCTTAGGTGGTCTCCAGTGGTGCCCAGCCGTAAAACCCGCTTATCATGCACCCCCCCTAAGAGATTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAAGCATATCAA-- Phaeothyriolum_dunnii_CPC_35847 -----------------------------------------------------------------ACTCTGGAGCAGACCCCCCACCCCCCCAGAACCACGCTGACCAGAAGTTTAGTGAACCTGCGGAAGGATCATTAATAGA--AGGCGCCCC----------CGGGCGCCGAAACCAAAAAAAATC--TGCCGTTCCCACAAGCATTTGG----------TAGGGGTTGTCCCCGCC----AGAGTCCCAAA-------CTTTGCGAAACCA-CGCGG---------------------------------------TCAAAGGACGAGAAGCAACAAAGCAAAAACTTTCAACAACGGATCTCTTGGTTCCAGCAACGATGAAGAACGCAGCAAAATGCGAGACGCGGTGCGAACTGCAG---TTAGTGAGTCATCGAAGTTTTGAACGCACATTGCGCCCTGGCCTTGTTGGCCGGTTCAAGGGGCACGTATGGTCGAGCGCCTTTTG--AAAATCAAG---CCCCCCACGCTTGGAATGGGG---CCGCCCCTC--GCGGCG-GCCCCGAAACTGACGGGCG--CCCCC--GGAGGCCGTCGAGCGGAACAG--GACCCGCACGTCGGCTGCCCCCGGGCG---------GCGGACCCC--------CGAAAACC---TCAAGTTTTGGCCTC-AACCTGTCGAGGATACCCGCTGAACTTAAGCATATCAATA Phaeothyriolum_eucalyptorum_HPC_2269 GGGAGGTTGGCAACGACCACCCTGGGCTGGGAAGTTGGTCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCG----------------------------TAGGTGAACCTGCGGAAGGATCATTAGAAGTGGAGGCGCCCC------CCCCCGGGCGCCCGTCCC---GTACATC--TGCCGTCCACACAAGCTTTTGG----------TAGGGGCCGTCCCCGCC----AGAGTCCCAAA-------CGCTGAGGAACCG-TACCG---------------------------------------TCCAAGCGCGAGC--GAGAAGAGCGAAAACTTTCAACAACGGATCTCTTGGTTCCAGCAACGATGAAGAACGCAGCAAAATGCGAGACGCGGTGCGAACTGCAG---TTAGTGAGTCATCGAAGTTTTGAACGCACATTGCGCCCTGGCC-CACGGCCTGATGCAAGGGGCACGCATGGTCGAGCGCCTTTTGAAAAACTCAAG---CCCCCCCAGCTTGGAATGGGG---TGGCCCCCCCCGTGGCC-GCCCCCAAACCGTCGGGCA-CCCCCCTAGCCGGACGCCGAGCGGAACAG--ACCCCGCGCGC-GGCGGTCCCTAGGGGA--------GTC?????????????????????????????????????????????????????????????????????????????---- Phaeothyriolum_amygdalinum_CPC_36084 -----------------------------------------------------------------------------------------------------------------????????????????????????????????GAGGCGCCCCCCTCCCCCGGGGGGCGCCCGTCCC---AAACATC--TGCCGTCCGCACAAGCTTTTGG----------TAGGGGCTGTCCCCGCC----AGAGTCCCAAA-------CGCCGAGGAACCACTGCCG---------------------------------------TCTAAGCGCGAGC--GAGAAGAGCGAAAACCTTCAACAACGGATCTCTTGGTTCCAGCAACGATGAAGAACGCAGCAAAATGCGAGACGCGGTGCGAACTGCAG---TTAGTGAGTCATCGAAGTTTTGAACGCACATTGCGCCCTGGCC-CACGGCCTGATGCAAGGGGCACGCATGGTCGAGCGCCTTTTG-AGAACTCAAG---CCCCTCCAGCTTGGAATGGGG---TGGCCCCCCC-GCGGCC-GCCCCGAAACCGTCGGGCACCCCCCCTAGCCGGCCGTCGAGCGGAACAG--ACCCCGCGCGT-GGCGGTCCCCAGGGGGGG------GTCAACCCCCCTCGGAGCGAA-------TAAAGGTTTGGCCTC-AACCTGT?????????????????????????????---- Phaeothyriolum_corymbiae_CPC_35789 ------------------------------------------------------------------------AACAAGGTTTCCG----------------------------TAGGTGAACCTGCGGAAGGATCATTAGAGGT-TAGGCGCCCC---CCCAACCCGGGGGCCCGTCCC---AAACACC--TGCCGTCCACACAAGCTTTTGG----------TAGGGGCTGTCCCCGCC----AGAGTCCTAAA-------CGTCGAGGAGCAA-TGCCG---------------------------------------TCTAAGCGCGAGC--GAGAAGAGCGAAAACTTTCAACAACGGATCTCTTGGTTCCAGCAACGATGAAGAACGCAGCAAAATGCGAGACGCGGTGCGAACTGCAG---TTAGTGAGTCATCGAAGTTTTGAACGCACATTGCGCCCTGGCC-CACGGCCTGATGCAAGGGGCACGCATGGTCGAGCGCCTTTTG-AAAACTCAAGCCCCCCCCCCAGCTTGGAATGGGG---TGGCCCCCC--TTGGCC-GCCCCGAAACCGTCGGGCA-CCCCCCTAGCTGGCCGTCAAGCGGAACAG--ACCCCGCGCGT-GGCGGTCCCTAGGGG---------GTCAACCCCCCTCGGAGCGA--------CAAAGGTTTGGCCTC-AACCTGTCGAGGATACCCGCTGAACTTAAGCATATC---- Phaeothyriolum_corymbiae_MG386045.1 ----------------------------------------------------------------------GTAACAAGGTTTCCG----------------------------TAGGTGAACCTGCGGAAGGATCATTAGAGGT-TAGGCGCCCC---CCCAACCCGGGGGCCCGTCCC---AAACACC--TGCCGTCCACACAAGCTTTTGG----------TAGGGGCTGTCCCCGCC----AGAGTCCTAAA-------CGTCGAGGAGCAA-TGCCG---------------------------------------TCTAAGCGCGAGC--GAGAAGAGCGAAAACTTTCAACAACGGATCTCTTGGTTCCAGCAACGATGAAGAACGCAGCAAAATGCGAGACGCGGTGCGAACTGCAG---TTAGTGAGTCATCGAAGTTTTGAACGCACATTGCGCCCTGGCC-CACGGCCTGATGCAAGGGGCACGCATGGTCGAGCGCCTTTTG-AAAACTCAAG-CCCCCCCCCAGCTTGGAATGGGG---TGGCCCCCC--TTGGCC-GCCCCGAAACCGTCGGGCA-CCCCCCTAGCTGGCCGTCAAGCGGAACAG--ACCCCGCGCGT-GGCGGTCCCTAGGGG---------GTCAACCCCCCTCGGAGCGA--------CAAAGGTTTGGCCTC-AACCTGTCGAGGATACCCGCTGAACTTAAGCATATC---- ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 740; 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 = PhaeothyriolumITSparsimony.trees; PSCORES 1 / TL = yes CI = yes RI = yes RC = yes HI = yes; Contree ALL / strict = yes treefile = PhaeothyriolumITSparsimonycons.tre; Bootstrap nreps = 1000 search = heuristic; Savetrees from = 1 to = 1 format = nexus brlens = yes savebootp = nodelabels maxdecimals = 0 file = PhaeothyriolumITSparsimonybootstrap.tre; Log stop = yes; END; BEGIN SETS; CHARSET combined = 114 - 282 321 - 736; TAXSET outgroups = 1; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 740; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 740; END; BEGIN TREES; Title 'Trees from "Fig 81.trees"'; ID 016e132be4961; LINK Taxa = Taxa; TRANSLATE [0] 1 'Melanconiella hyperopta NR_160258.1', [1] 2 Phaeothyriolum_dunnii_CPC_35847, [2] 3 Phaeothyriolum_eucalyptorum_HPC_2269, [3] 4 Phaeothyriolum_amygdalinum_CPC_36084, [4] 5 Phaeothyriolum_corymbiae_CPC_35789, [5] 6 Phaeothyriolum_corymbiae_MG386045.1; TREE Fig._81 = (((((5:1,6:0.0):17,4:17):5,3:14):35,2:58):110,1:107):0.0; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1572279783748; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 3224460016425675526; tell It; setDefaultOrder 5 4 3 2 0 1; attachments ; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 5385261600258556534; mqVersion 340; checksumv 0 3 505673422 null getNumChars 740 numChars 740 getNumTaxa 6 numTaxa 6 short true bits 15 states 15 sumSquaresStatesOnly 55327.0 sumSquares 55327.0 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 2575 839; setLocation 8 23; setFont SanSerif; setFontSize 18; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #3224460016425675526 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; setTreeBlockID 016e132be4961; toggleUseWeights off; endTell; setAssignedID 996.1572279681550.4785372730198883117; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1966 767; setLocation 8 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 '(1:107,(2:58,(3:14,(4:17,(5:1,6:0.0):17):5):35):110):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 #5385261600258556534 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 657; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1966 767; setLocation 8 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;