#NEXUS [written Fri Jan 19 14:09:55 CET 2018 by Mesquite version 3.04 (build 725) at DSK-SAMS-018/10.136.121.36] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=11; TAXLABELS 'Talaromyces aerugineus CBS_350.66 KJ885285' 'Talaromyces diversiformis DTO_317-E3 KX961259' 'Talaromyces bohemicus CBS_545.86 KJ885286' 'Talaromyces cinnabarinus CBS_267.72 KJ885256' 'Talaromyces boninensis CBS_650.95 KJ885263' 'Talaromyces reverso-olivaceus DTO_317-C3 KU866730' 'Talaromyces helicus CBS_335.48 KJ885289' Talaromyces_species_URM_7624 Talaromyces_borbonicus_CBS_141340 'Talaromyces varians CBS_386.48 KJ885284' 'Talaromyces adpressus DTO_317-G4 KU866741' ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=578; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX 'Talaromyces aerugineus CBS_350.66 KJ885285' gaaattatttccttt-tccccatgat--------------------------ttggct---tgtcggatttgaccatatctaacgcgttgctggtgaacaggacaaggatggcgatggtgagtc-----gagataccttt--------------tgcgcaagcgatgaaatccgttt-----------------catggacagaaaat---------ttttaac---------attgc---ctatgatcaggtcaaatcacaacaaaggaattgggcaccgttatgcgctctctcggccagaacccttccgagtctgaattgcaggacatgatcaacgaagtcgacgctgacaacaacggcacaatcgatttccctggtatgatcaact--------------------------------------actcatatcttgatggtata----------------------tttttagtttggataa--ctcataaatgg-tagaatttttgacaatgatggcccgcaaaatgaaggacaccgactccgaggaagaaattcgtgaagctttcaaggtgtt 'Talaromyces diversiformis DTO_317-E3 KX961259' gaaattatttattgt-cccccataat--------------------------atgact---tgtcggatttgatcatgtctaacgcgttgtttgtgaacaggacaaggatggcgatggtgagtc-----gagataccttc--------------tacgcaagcgatggaatatgttt-----------------agtagacaggag-----------ttttaat---------attgc---ctctgatcaggtcaaatcacaacaaaggaattgggcaccgtcatgcgctctctcggtcagaacccttccgagtctgaattgcaggacatgatcaacgaagtcgacgctgacaacaacggcacaatcgatttccctggtatgaccaact------------------------------------acactcacatcttgatggtctattttt-----------------tttttggtttggataa--ctcataaatgg-tagaattcttgacaatgatggcccgcaaaatgaaggacaccgactccgaggaagaaattcgcgaagctttcaaggtgtt 'Talaromyces bohemicus CBS_545.86 KJ885286' gaaattatttccttt-tccctattat--------------------------ttggct---tgtcggatttgaccatgtctaacgcgttacttgtgaacaggacaaggatggcgatggtgagtc-----aagataccttc--------------tgcgcaagcgatgaaatccgttt-----------------catggacagattt----------ttttaac---------attgg---ttttgatcaggtcaaatcacaacaaaggaattgggcaccgttatgcgctctctcggccagaacccttccgagtctgaattgcaggacatgatcaacgaagtcgacgctgacaacaatggcacaatcgatttccctggtatggcaa---------------------------------------ctaatcacatcctgatggtctgttatc-----------------------ggttggataa--ctcataaatgg-tagaatttttgacaatgatggcccgcaaaatgaaggacaccgactccgaggaagaaatccgcgaagctttcaaggtgtt 'Talaromyces cinnabarinus CBS_267.72 KJ885256' gtaatatttcttttt-ttcccgcaa---------------------------ttgttg---ggttgtatataca---ttctaacgcgctgctcgtgaacaggacaaggatggggatggtgagtt-----gagatgcctct--------------tgcgcaagcgatg-aatctattt-----------------cacgaacagaaa------------tttaat---------attgt-----ctgatcaggtcaaatcacaacaaaggaattgggtaccgtcatgcgctctctcggccagaatccttccgaatcggaattgcaggacatgatcaacgaggttgacgcggacaacaatggcacaatcgatttccctggtatgaaac---------------------------------------cttatcacaacctggta---------------------------tttgggtattggataa--ctca-tgatga-tagaattcttgacaatgatggctcgcaaaatgaaggataccgactctgaggaagaaattcgcgaagctttcaaagtttt 'Talaromyces boninensis CBS_650.95 KJ885263' gtgtctaccaagctc-ttgttatggcgaccggtttgacggtttgagaaagaattgtgt---gacagtaatctaatctttttttggtcttgatgatttacaggacaaagatggcgatggtgagtttttc-gagagcatttactccgaattgcagataagcaatcgacgagga----------------------------atacgaatctatccgaaattgtact-aaagcgtgatggatgttgttggtcaggtcaaatcacaaccaaagaactcggtaccgtcatgcgttctctcggccagaacccttccgaatccgaattgcaggacatgatcaacgaagtcgacgctgacaacaacggcacaattgactttcctggtatgatcaaat------------------------------ccgccctcactcccactctttccccagctcctt------------------ccgcagtgtgattaa-tcgaaagggttt-tagaattcttgaccatgatggctcgcaaaatgaaggataccgactccgaagaagaaattcgtgaggcattcaaggtgtt 'Talaromyces reverso-olivaceus DTO_317-C3 KU866730' gtgtctaccaacctc-ttgttatggcgaccggtttgacggtttgagcaagaattgtgt---ggcagtaatctaacctttttttggtcttgatgatgtacaggacaaagatggtgatggtgagtttttc-gagagcatttattccgaattgcagataagcaatcaacgaaga----------------------------atacgaatctatccgaaattgtact-aaagcgtgatgga---cgtttgccaggtcaaatcacaaccaaagaactcggtaccgtcatgcgttctctcggccagaacccttccgaatccgaattgcaggacatgatcaacgaagtcgacgctgacaacaacggcacaatcgactttcctggtatggcccaat------------------------------tcgccctcactcccgctctttccccagttccct------------------ccgcagtgtgattaa-tcgaaagggtat-tagaattcttgaccatgatggctcgcaaaatgaaggataccgactccgaagaagaaattcgtgaggcattcaaggtgtt 'Talaromyces helicus CBS_335.48 KJ885289' gtacccaccaagctc-ttgttatggcgaccggtttgacggtttgagcaagaattgtgt---ggcagcaatctaa---tattttgatcttgatgatgtacaggacaaagatggcgatggtgagtttgtc-gagagcatttactccgaattgcagataagcaatcaacgaaga----------aaaaaggggtcgacatggacacaaacctgtggaatactgtactaaaagcgtgatcga---cgttggccaggtcaaatcacaaccaaagaactcggtaccgtcatgcgctctctcggccagaacccttccgaatccgaattgcaggacatgatcaacgaagtcgacgctgataacaacggcacaattgactttcctggtatgatcaaaat-----------------------------ccgtcctcactcccgctgttttgccagctccccc----------------ctcgcagtgtgattaa-tagaaagggtat-tagaattcttgaccatgatggctcgcaaaatgaaggataccgactccgaagaagaaatccgcgaggcattcaaggtgtt Talaromyces_species_URM_7624 gtcccgatcaagcct-ttgttatcgctatcggtt----------gagaagaattgtgc--aggcagtaatctaa---ccttttgg---tcttgatggacaggacaaagatggcgatggtgagttttt--gagtccactcac-tccga-tgcagacgaa-aatcaacg---------------agaagagaccagcatgaatagaagtt--gagaatgccgtact--aagcgtaatcga---cattggtcaggtcaaatcacaaccaaagaactcggtaccgtcatgcgctctctcggccagaacccttccgaatccgaattgcaggacatgatcaacgaagtcgacgctgataataacggcacaattgactttcctggtacgatcaataactctcctcttcaatggctttgttttgtctttgtccttggccttgtgtttttatta-tttgttcgaatccctgtctgccctcgacaataatattga--cg-gatggtat-tagaattcttgactatgatggctcgcaaaatgaaggataccgattccgaagaagaaatccgcgaggcattcaaggtgtt Talaromyces_borbonicus_CBS_141340 gtgccgatcaagcct-ttgttattgcgatcggtt----------gagaagaattgtgc--agggagtaatctaa---ccttttgg---tcttgatggataggacaaagatggcgatggtgagtcttt--gagaccgtccacatcgaa-tccagacgagcaatcaacg---------------agaagagaccagcgtgaatagaagt---gagaataccgtact--aagcgtgatcga---tattggtcaggtcaaattacaaccaaagaactcggtaccgtcatgcgctctctcggccagaacccttccgaatccgaattgcaggacatgatcaacgaagtcgacgctgataataacggcacaattgactttcctggtacgatcaataactctcctcttcaatggcttggttttgtctttgtctttggccttgtgttttcactattttgttcaaatcccttgtcagc--cgacaataagattga--cgaaatggtat-tagaattcttgactatgatggctcgcaaaatgaaggataccgattccgaagaagaaatccgcgaggcattcaaagtgtt 'Talaromyces varians CBS_386.48 KJ885284' gtgccgtccaagctctttgttatggcgaccggtttgacagtttgagatggaattttgtggtggcagtaatctaa---ccttttgg---tcttgatgtataggataaagatggcgatggtgagtctttctgagatcacctcattccgaactcggatatgcaatcaaatgaag-----------aaaaggagtcggcatgagtacaaaaccatgaaataccgtaac-taagcgtgttcga---tattggccaggtcaaatcacaaccaaagaactcggcaccgttatgcgctctctcggccagaatccttccgaatccgaattgcaggacatgatcaacgaagtcgacgctgataacaacggcacaattgacttccctggtacgataaacccctttcgtcttcg---------------cactgtcaatggtct-----------------------atgttgtgtcagc--cggcagtgtgatttaacagaaataatgtctagaattcttgaccatgatggctcgcaaaatgaaggacaccgactctgaagaagaaatccgcgaggcactcaaggtgtt 'Talaromyces adpressus DTO_317-G4 KU866741' gt----ttggaaatc-tggttgtcgca------------------------atgttgt---ggtggatggttag---ctgactagccgttttgatgagtaggacaaggatggtgatggtgagtccgcc---------------------------acgaacacgacgatatttgtctcgagcaaaggtttttttcacgagcatatatt-------------------------gataa---aatccaataggccaaattacaaccaaggaactgggcaccgttatgcgttccctcggccagaacccctccgaatccgaactgcaggacatgatcaacgaagtcgacgctgacaacaacggcacaatcgatttccctggtatgatataat-------------------------------------tggtcacgggttaata----------------------------cgatggcagtactaa-------ctgccg-cagaattcttgacaatgatggcccgcaaaatgaaggataccgactccgaggaagagatccgtgaagctttcaaggtgtt ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 578; END; BEGIN NOTES; TAXABITS TAXA = Taxa NAME = newlyAddedTaxon on = 1 - 11; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 578; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 578; END; BEGIN TREES; Title 'Trees from "20170530 CaM Helici ML.nwk"'; LINK Taxa = Taxa; TRANSLATE [0] 10 'Talaromyces aerugineus CBS_350.66 KJ885285', [1] 9 'Talaromyces diversiformis DTO_317-E3 KX961259', [2] 11 'Talaromyces bohemicus CBS_545.86 KJ885286', [3] 8 'Talaromyces cinnabarinus CBS_267.72 KJ885256', [4] 1 'Talaromyces boninensis CBS_650.95 KJ885263', [5] 2 'Talaromyces reverso-olivaceus DTO_317-C3 KU866730', [6] 3 'Talaromyces helicus CBS_335.48 KJ885289', [7] 4 Talaromyces_species_URM_7624, [8] 5 Talaromyces_borbonicus_CBS_141340, [9] 6 'Talaromyces varians CBS_386.48 KJ885284', [10] 7 'Talaromyces adpressus DTO_317-G4 KU866741'; TREE PHYLIP_1 = (7:0.283576,((6:0.056323,((3:0.011111,(1:0.015084,2:0.021389)0.9860:0.019924)0.9900:0.028301,(4:0.00819,5:0.015361)1.0000:0.063579)0.4740:0.021183)0.9990:0.134808,(8:0.134266,(9:0.042957,(10:0.015989,11:0.040885)0.7380:0.005245)0.9970:0.0593)1.0000:0.210605):0.0); END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1516367395751; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 162128872021147559; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 5698052990694612994; mqVersion 304; checksumv 0 3 5028363 null getNumChars 578 numChars 578 getNumTaxa 11 numTaxa 11 short true bits 1152921504606846991 states 15 sumSquaresStatesOnly 113587.0 sumSquares -2.658636989623389E21 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 253; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1750 983; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #162128872021147559 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #162128872021147559; getWindow; tell It; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1497 911; setLocation 8 8; 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 #162128872021147559 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1673.1516367262472.4863511522437848853; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1497 911; 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; 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 #5698052990694612994 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1497 911; setLocation 8 8; 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;