#NEXUS [written Fri Jan 19 14:28:08 CET 2018 by Mesquite version 3.04 (build 725) at DSK-SAMS-018/10.136.121.36] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=12; TAXLABELS 'Talaromyces aerugineus CBS_350.66 AY753346' 'Talaromyces diversiformis DTO_317-E3 KX961215' 'Talaromyces ryukyuensis NHL_2917 AB176628' 'Talaromyces bohemicus CBS_545.86 JN899400' 'Talaromyces cinnabarinus CBS_267.72 JN899376' 'Talaromyces boninensis CBS_650.95 JN899356' 'Talaromyces helicus CBS_335.48 JN899359' Talaromyces_species_URM_7624 'Talaromyces reverso-olivaceus DTO_317-C3 KU866646' 'Talaromyces adpressus DTO_317-G4 KU866657' Talaromyces_borbonicus_CBS_141340 'Talaromyces varians CBS_386.48 JN899368' ; END; BEGIN CHARACTERS; TITLE Character_Matrix; LINK TAXA = Taxa; DIMENSIONS NCHAR=455; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX 'Talaromyces aerugineus CBS_350.66 AY753346' tctcccacccgtgtcg-ttg--ataacctgttgcttgggcgggcccaccaggttctccctggtcgccggggggcatc-gcccccgggcccgcgcccgccgaagcaccctaggaactctgatgaagat-aggctgtctgagtctgacg-aaaaattgtcaaaactttcaacaatggatctcttggttccggcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattccgtgaatcatcgaatctttgaacgcacattgcgccccctggcattccggggggcatgcctgtccgagcgtcatttctgccctcaagcgcggcttgtgtgttgggcgtggtcccccc-ggggacctgcccgaaaggcagcggcgacgtccgtcgggtcctcgagcgtatggggctttgtcactcgctcgggagggacctgcgggggttggtcac 'Talaromyces diversiformis DTO_317-E3 KX961215' tctcccacccgtgtcg-ttg--ataacctgttgcttgggcgggcccaccgggttctgcctggtcgccggggggcatc-gcccccgggcccgcgcccgccgaagcaccctaggaaccctgatgaagat-aggctgtctgagtctgacgaaaaaattgtcaaaactttcaacaatggatctcttggttccggcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattccgtgaatcatcgaatctttgaacgcacattgcgccccctggcattccggggggcatgcctgtccgagcgtcatttctgccctcaagcgcggcttgtgtgttgggcgtggtcccccc-ggggacctgcccgaaaggcagcggcgacgtccgtcgggtcctcgagcgtatggggctttgtcactcgctcgggagggacctgcgggggttggtcac 'Talaromyces ryukyuensis NHL_2917 AB176628' tctcccacccgtgtcgtttg--ataacctgttgcttgggcgggcccaccgggttctgcctggtcgccggggggcatc-gcccccgggcccgcgcccgccgaagcaccctaggaactctgatgaagat-gggctgtctgagtctgacgaaacaattgtcaaaactttcaacaatggatctcttggttccggcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattccgtgaatcatcgaatctttgaacgcacattgcgccccctggcattccggggggcatgcctgtccgagcgtcatttctgccctcaagcgcggcttgtgtgttgggcgtggtcccccc-ggggacctgcccgaaaggcagcggcgacgtccgtcgggtcctcgagcgtatggggctttgtcactcgctcgggagggacctgcgggggttggtcac 'Talaromyces bohemicus CBS_545.86 JN899400' tctcccacccgtgtcg-ttg--ataacctgttgcttgggcgggcccaccg?gt--cacctggtcgccg?ggggcatc-gcccccgggcccgcgcccgccgaagcaccctaggaaccctgatgaagat-aggctgtctgagc-tgacg-aaaaattgtcaaaactttcaacaatggatctcttggttccggcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattccgtgaatcatcgaatctttgaacgcacattgcgccccctggcattccggggggcatgcctgtccgagcgtcatttctgccctcaagcgcggcttgtgtgttgggcgtggtcccccc-ggggacctgcccgaaaggcagcggcgacgtccgtcgggtcctcgagcgtatggggc-ttgtcactcgctcgggagggacctgcgggggttggtcac 'Talaromyces cinnabarinus CBS_267.72 JN899376' cctcccacccttgtcg-ttg----aacctgttgctttggcgggcccaccggggccaacctggtcgccgggggacac--gtccccgggcccgcgcccgccgaagcaccctaagaactctgatgaagtt-gggctgtctgagt-cgatatgaaaattgtcaaaactttcaacaatggatctcttggttccggcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattccgtgaatcatcgaatctttgaacgcacattgcgccccctggcattccggggggcatgcctgtccgagcgtcatttctgccctcaagcgcggcttgtgtgttgggcgtggtcccccc-ggggacctgcccgaaaggcagcggcgacgtccgttgggtcctcgagcgtatggggc-ttgtcactcgctcgggaaggacctgcgggggttggtcac 'Talaromyces boninensis CBS_650.95 JN899356' cctcccacccgtgccg-ttat-aatacctgttgctttggcgggcccaccgggg--cacctggtcgccgggggacgtc-gtccccgggcccgcgcccgccgaagcaccccctgaactctgaagaagatagggctgtctgag---acctagaaaattgtcaaaactttcaacaatggatctcttggttccggcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattccgtgaatcatcgaatctttgaacgcacattgcgccccctggcattccggggggcatgcctgtccgagcgtcatttctgccctcaagcacggcttgtgtgttgggtgtggtcccccc-ggggacctgccccaaaggcagcggcgacgcccgtcgggtcctcgagcgcatggggc-ttgtcactcgctcgggagggacctgcgggggttggtcac 'Talaromyces helicus CBS_335.48 JN899359' cctcccacccgtgccg-ttat-aatacctgttgctttggcgggcccac--gggg-cacctggtcgctgggggacgcc-gtccccgggcccgcgcccgccgaagcaccccctgaactctgaagaagatagggctgtctgag---acctagaaaattgtcaaaactttcaacaatggatctcttggttccggcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattccgtgaatcatcgaatctttgaacgcacattgcgccccctggcattccggggggcatgcctgtccgagcgtcatttctgccctcaagcacggcttgtgtgttgggtgtggtccccccgggggacctgccccaaaggcagcggcgacgcccgtcgggtcctcgagcgcatggggc-ttgtcacttgctcgggagggacctgcgggggttggtcac Talaromyces_species_URM_7624 cctcccacccgtgtcg-ttatgaatacctgttgctttggcgggcccaccggggc-tgcctggtcgccgggggacgcctgtccccgggcccgcgcccgccgaagcaccccctgaactctgaagaagatagggctgtctgag--tacctagaaaatagtcaaaactttcaacaatggatctcttggttccggcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattccgtgaatcatcgaatctttgaacgcacattgcgccccctggcattccggggggcatgcctgtccgagcgtcatttctgccctcaagcccggcttgtgtgttgggtgtggtcccccc-ggggacctgccccaaaggcagcggcgacgcccgtcgggtcctcgagcgcatggggctttgtcactcgctcgggagggacctgcgggagtcggtcac 'Talaromyces reverso-olivaceus DTO_317-C3 KU866646' cctcccacccgtgccg-ttat-catacctgttgctttggcgggcccaccggggt-tacctggtcgccgggggacgtctgtccccgggcccgcgcccgccggagcaccccctgaactctgaagaagatagggctgtctgag--tacctagaaaattgtcaaaactttcaacaatggatctcttggttccggcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattccgtgaatcatcgaatctttgaacgcacattgcgccccctggcattccggggggcatgcctgtccgagcgtcatttctgccctcaagcacggcttgtgtgttgggtgtggtcccccc-ggggacctgccccaaaggcagcggcgacgcccgtcgggtcctcgagcgcatggggctttgtcactcgctcgggagggacctgcgggggttggtcac 'Talaromyces adpressus DTO_317-G4 KU866657' cctcccacccttgtct-ctat--acacctgttgctttggcgggcccaccggggc-cacctggtcgccgggggacgcacgtccccgggcccgcgcccgccgaagcgctctgtgaaccctgatgaagat-gggctgtctgag--tactatgaaaattgtcaaaactttcaacaatggatctcttggttccggcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattccgtgaatcatcgaatctttgaacgcacattgcgccccctggcattccggggggcatgcctgtccgagcgtcatttctgccctcaagcacggcttgtgtgttgggtgtggtcccccc-ggggacctgcccgaaaggcagcggcgacgtccgtctggtcctcgagcgtatggggctctgtcactcgctcgggagggacctgcgggggttggtcac Talaromyces_borbonicus_CBS_141340 ctccccacccgtgtcg-ttatgaatacctgttgctttggcgggcccaccggggc-tgcctggtcgccgggggacgcctgtccccgggcccgcgcccgccgaagcaccccctgaactctgaagaagatagggctgtctgag--tacctagaaaatagtcaaaactttcaacaatggatctcttggttccggcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattccgtgaatcatcgaatctttgaacgcacattgcgccccctggcattccggggggcatgcctgtccgagcgtcatttctgccctcaagcccggcttgtgtgttgggtgtggtcccccc-ggggacctgccccaaaggcagcggcgacgcccgtcgggtcctcgagcgcatggggctttgtcactcgctcgggagggacctgcgggagtcggtcac 'Talaromyces varians CBS_386.48 JN899368' cctcccacccgtgtcgttttttaacacctgttgctttggcaggcccactggggg-cccccggtcgcctgcggacgcgcgtcctcgggcctgcgcctgccagagcaccccctgaactctgaagaagatagggctgtctgag---acctagaaaattgtcaaaactttcaacaatggatctcttggttccggcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattccgtgaatcatcgaatctttgaacgcacattgcgccccctggcattccggggggcatgcctgtccgagcgtcatttctgccctcaagcgcggcttgtgtgttgggtgtggtcccccc-ggggacctgccccaaaggcagcggcgacgcctgttgggtcctcgagcgcatggggc-ttgtcactcgctcgggagggacc-gcgggcgttggtcac ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 455; END; BEGIN NOTES; TAXABITS TAXA = Taxa NAME = newlyAddedTaxon on = 1 - 12; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 455; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 455; END; BEGIN TREES; Title 'Trees from "20170530 ITS Helici ML Phylogeny.nwk"'; LINK Taxa = Taxa; TRANSLATE [0] 3 'Talaromyces aerugineus CBS_350.66 AY753346', [1] 1 'Talaromyces diversiformis DTO_317-E3 KX961215', [2] 4 'Talaromyces ryukyuensis NHL_2917 AB176628', [3] t4t 'Talaromyces bohemicus CBS_545.86 JN899400', [4] 5 'Talaromyces cinnabarinus CBS_267.72 JN899376', [5] 11 'Talaromyces boninensis CBS_650.95 JN899356', [6] 10 'Talaromyces helicus CBS_335.48 JN899359', [7] 8 Talaromyces_species_URM_7624, [8] 12 'Talaromyces reverso-olivaceus DTO_317-C3 KU866646', [9] 6 'Talaromyces adpressus DTO_317-G4 KU866657', [10] 9 Talaromyces_borbonicus_CBS_141340, [11] t12t 'Talaromyces varians CBS_386.48 JN899368'; TREE PHYLIP_1 = (6:0.021335,((5:0.010435,(4:0.002704,(3:0.002352,(1:0.0)0.4540:0.002323)0.4700:0.002001)1.0000:0.0334)0.9320:0.025091,(10:0.043105,((8:0.0,9:0.004704)0.9990:0.014814,((11:0.0,12:0.004687)0.5110:0.002345)0.7750:0.002501)0.6000:0.0)0.9860:0.025753):0.0); END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1516368489056; linkFile 20180118_ITS_Helici_TreeBASE.nex; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 2068286826333311682; setID 1 3242259466717923642; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 507831608646882486; mqVersion 304; checksumv 0 3 3676195944 null getNumChars 455 numChars 455 getNumTaxa 12 numTaxa 12 short true bits 1152921504606846991 states 15 sumSquaresStatesOnly 107334.0 sumSquares -5.506353106002301E21 longCompressibleToShort false usingShortMatrix true NumFiles 2 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 253; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1525 853; setLocation 547 318; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #2068286826333311682 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #2068286826333311682; getWindow; tell It; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1272 781; setLocation 547 318; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.ibeam; endTell; endTell; showWindow; getEmployee #mesquite.lists.ColorTaxon.ColorTaxon; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #2068286826333311682 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTaxa #2068286826333311682; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1974.1516284161742.4531874304001732562; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1272 781; setLocation 547 318; 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; 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 #507831608646882486 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 200; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1272 781; setLocation 547 318; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; 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;