#NEXUS [written Sat Jun 22 15:10:09 EEST 2013 by Mesquite version 2.75 (build 564) at Eugene-PC/127.0.0.1] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=10; TAXLABELS Hyphodontia_subalutacea_DQ340341 Hyphodontia_floccosa_DQ873618 Fibrodontia_alba_KC928274 Fibrodontia_alba_JQ612713 Fibrodontia_gossypina_DQ249274 Fibrodontia_brevidens_KC928276 Trechispora_farinacea_EU909231 Subulicystidium_longisporum_JQ905612 Porpomyces_mucidus_FJ496660 Sistotremastrum_suecicum_EU118666 ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=585; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Hyphodontia_subalutacea_DQ340341 -----------AAATCCACTCAA-CCACTGTGCACTAATTCGAAGCTTTGCGGTT----------------------------CAGGCTCCCTTCGGGTTGAGTTCGGGCTTGCG-----GGGTTTTCGAGCTTCATACAAACCACTATATTGTCATGTCG----AATGTAATACTTTAATAAAATACAACTTTCAACAAC-------------GGATCTCTTGG-CTCTCG-CATCGATGAAGAACGCAGC-GAAATGCGATAAGTAATGTGAATT-GCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCT-----CTTTGGTATTCCGAAGAGCATGCCTGTTTGAGTGTCATGTAATCATCAATCCGACTTTG----CTTTTTTGTAAAGT-CCGGACTTGGATTTGGAGGTTATTGCTGCTTTC---CG-TCGGCTCCTCTTGAATGCATTAGTTGGACTCCGTCGCGG--------TTCGCGGTGTGATAATTTATTCACTC----------------------------------------TTGAACTTCGAAGTAGACCGCGTCTAAC Hyphodontia_floccosa_DQ873618 --------GCTCAATCCACTCAA-CCACTGTGCACTAATTCGAAGCTTCGCGGTCCTCCCGAACCTGGTTCGGGAGCAGCTCCCCCTTTCGCGAGGGGTTGAGTCGGGGCCTGCG-----GGGTTTCGAGCCTTCATACAAACCACT-TCTTGTCATGTAG----AATGTTATTATATTGAAAAATACAACTTTCAACAAC-------------GGATCTCTTGG-CTCTCG-CATCGATGAAGAACGCAGC-GAAATGCGATAAGTAATGTGAATT-GCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCT-----CCTTGGTATTCCGAGGAGCATGCCTGTTTGAGTGTCATGTAATCATCAACCTCCCTTCG----CTTTTGCGTTCGGG-ATGGCTTGGAATTGGAGGTTTCTTGTCGCTCTCGCGAG-TCGGCTCCTCTTGAAGACATTAGTCGGACTCGGTCGCTCCGTCGCGGTACGCGGTGTGATAACTTATTCACCCATCGGTAAAC------------------------------CCGCCTCTTGCGTCCGGCTGCTTCTAAC Fibrodontia_alba_KC928274 GATTCCCCGTCCA---CACCAAACCCCCTGTGCACCTTTC--------------TCGATGGGAAA------------------TGCGG-CTTCGCGGCCGCAAAGTACCGTCGC------CGTCTCACAAACGCTTCGTAAACGTACACGGAATGAATGCGCGGTGCTCCGCGACTAAAACACAAAACAACTTTCAACAAC-------------GGATCTCTTGG-CTCTCG-CATCGATGAAGAACGCAGC-GAAATGCGATAAGTAATGTGAATT-GCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCC-----CCTTGGCATTCCGAGGGGCATGCCCGTTTGAGTGTCTTGAATTCATCCTCCCGCCG-------GTTTCGCGACC-GG-TCGGGTTGGGACTTGGGGG--TTTGCGCCGCGTGAGCG-GAGGCTCCCCTTGAATGCATCGGTGGGATTTTGCCGGGC--CGCATCCCTTGGGCGTTGTATTGTCCTCGTCCGCAGC-----GGATTGCCCCGGCGTCGCCCGCC-------TAGACCTTGCCTTTCGAGAGCGGTCAAC Fibrodontia_alba_JQ612713 GATTCCCCGTCCA---CACCAAA-CCCCTGTGCACCTTTC--------------TCGATGGGAAA------------------TGCGG-CTTTGCGGCCGCAAAGTACCGTCGC------CGTCTCACAAACGCTTTGTAAACGTACATGGAATGAATACGCGGTGCTCCGCGACT-AAACACAAAACAACTTTCAACAAC-------------GGATCTCTTGG-CTCTCG-CATCGATGAAGAACGCAGC-GAAATGCGATAAGTAATGTGAATT-GCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCC-----CCTTGGCATTCCGAGGGGCATGCCCGTTTGAGTGTCTTGAATTCATCCTCCCGCCG-------GTTTCGCGACC-GG-TCGGGCTGGGACTTGGGGG--TTTGCACCGCATGAGCG-GAGGCTCCCCTTGAATGTATCGGTGGGATTTTGCTGGGC--CGCATCCCTTGGGCGTTGTATTGTCCTCGTCCGCAGC-----GGATTGCCCCGGTGTCGCCCGCC-------TAGACCTTGCCTTTCGAGAGCGGTCAAC Fibrodontia_gossypina_DQ249274 GGCTTTCCGTCCA---CACCAAA-CCCCTGTGCACCTTTC-------------TCCGATGGGAAA------------------TGCGGCCGCTATGGTTGCAAAGTACCGTCGCA-----GCCTTCACAAACACTTTTCAAACGTCTATGGAATGCATTCGCGGTGCTCCGCGACTAAATCACAAAACAACTTTCAACAAC-------------GGATCTCTTGG-CTCTCG-CATCGATGAAGAACGCAGC-GAAATGCGATAAGTAATGTGAATT-GCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCC-----CCTTGGCATTCCGAGGGGCATGCCCGTTTGAGTGTCTTGAATTCATCCTCCCGTCG-------GTTTCGCGACC-TG-TCGGGTTGGGACTTGGGGGTCTTTGCTCCGCGTGAGCG-GTGGCTCCCCTCGAATGGATCGGTGGGATTTTGCCGGATTGCGCATCCCTTGGGCGTTGTATTGTCCTCGTCCGCAGC-----GGATTGCCCCGGCGTCGCCCGCT-------TCGACCTTGCCCGTAGAGGGCGGTCAAC Fibrodontia_brevidens_KC928276 GCCCGACCGTCCA---CACCAAA-CCCCTGTGCACCTTTC--------------TCGACGGGAAA------------------CGCGGCCCTCGCGGTCGCCGAGTACCGTCGC------CGATTCACAAACGCTTTGTAAACGTACGCAGAATGAACACGCGGTGCTCCGCGACTAAAACGAAAAACAACTTTCAACAAC-------------GGATCTCTTGG-CTCTCG-CATCGATGAAGAACGCAGC-GAAATGCGATAAGTAATGTGAATT-GCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCC-----CCTTGGCATTCCGAGGGGCATGCCCGTTTGAGTGTCTTGAATTCATCCTCCCGCCG-------GTTTCGCGACCGGG-TCGGGCAGGGACTTGGGGG--TTTGCACCGCGCGAGCG-GAGGCTCCCCTCGAATGGATCGGTGGGATTTGCAGGGTC---GCATCCCTTGGGCGTTGTATTGTCCTCGTCCGCAGC-----GGATTGCCCCGGCGTCGCCCGCC-------TCGACCTCGCCTTTGGAGAGCGGTCAAT Trechispora_farinacea_EU909231 GCGTGCGAGCCCGATCCGCTCAA-CCCTTACAAACCCACCGTGCACATTTGTCGGCGGAGGGCTCGGTCAAACGGGCCCCGAGCC-----------------------------------GGACCCACAAACCCC----AAGCATTAAAAGAATGACTAGCGGACGTTGTGCCGTCTAAACT-TTAACAACTTTCAACAAC-------------GGATCTCTTGG-CTCTCG-CATCGATGAAGAACGCAGC-GAAATGCGATAAGTAATGTGAATT-GCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCT-----CCTTGGTATTCCGAGGAGCATGCCTGTTTGAGTGTCTTGAAGTCATCAACCTCTCCC------GTTTTGCGACGGGT-CCGGGTTGGAGCCTGGGGG--ATTGCGCCGC----GAG-GCTGCTCCCCTCAAATGCATCGGTTGGGCCTGCGGGTCG---AACTCGGTTGGGCGTTGTACCATCCTCGCTCTTATCCCGAGATGTTCCCCCATTAATGTGCCCTCCCACGACCGCCCCCATTCTGGAGTCGCGGTCAAG Subulicystidium_longisporum_JQ905612 TGTCCCTTCTCTATTCCACC----CCACTGTGAACCAAG--------------------------------------------CGTGCGAGCAGAAGAGAGATCGGAAGCCCGCATGCTCACTTTAACATACCCCCGATTAAGTATCTGAATGT---------ACCTTGCGTTAACTCGCACAAATACAACTTTCAACAAC-------------GGATCTCTTGG-CTCTCG-CATCGATGAAGAACGCAGC-GAAATGCGATAAGTAATGTGAATT-GCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCC-----CCTTGGCATTCCGAGGGGCACGCCTGTTCGAGTGTCGTGAACTCCTCCACCCCCTAC------CTTTTTCGAAGGGTATCGGGCTGGGATTTGGGAG--CTTGCGGTCCCTGGCCGATCCGCTCTCCTTGAATGCATTAGCGAAGCCCTTGCGGCC-----------TTGGTGTGATAGTCATCTACGCCTCGGCTTAGCGAAT-----------------------------------CTATGGGAGTCCTTCCAAC Porpomyces_mucidus_FJ496660 --------GTCCAACCCTTCACA-CCCCTGTGCACCTTTTTAAAACCTTTC--TCTGGAGGGGGATGGCAAAAGGGCCGGCTGCGGGAACGCGGCGGGCCCCGATCCTCCCCACCTGGGGGGGTTTACAAACTCTGTCGAAACGCGTGTGTTGCGCGGCCTCCGTGCCGTCCTAACAAACTTTGTAACAACTTTCAACAAC-------------GGATCTCTTGG-CTCTCG-CATCGATGAAGAACGCAGC-GAAATGCGATAAGTAATGTGAATT-GCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCT-----CCTTGGTATTCCGAGGAGCATGCCTGTTTGAGTGTCTCGAAATCATCAGTCCCCCCGGGGTGCGTGCACCCTCGCGG-GCCGGATTGGACTTGGGGG--CCTGCTCCGA----GAG-GCGGCTCCCCTTAAATGCATCGGCGGCGGCCAGTCGACC----------CTTGGCGTTGTATCACCCTCGCCTC---------AGAGGCGACCAGTGCCCCGCCCC--------GACCTGCCCGTTTGGAGTGCGGTCAAA Sistotremastrum_suecicum_EU118666 GGGACGGGGTTAATCCCCACAAA-CCCTTGTGCACCATAGAGG-----------------------------------------------------------------------------GGACTTACGACCTACTCCAATATTCATATAATCTATACGACTGATGTCTTTTGTCTTTATCTATTATTAATAATAAACAATCTTTCAAACAACGAGATCTCTTGGACTCTCGTCATCGATGAAGAACGCAGCAGAAATGCGATAAGTAATGTGAATTAGCAGAATTCAGTGAATCATCGAATCTTATGACACGCACCTTGACGACTACCTTGGCATTCCGAGGAGCATGCCCGGG-----------------------------------------------------------------------TTTGCTGCTTTTCGGAG-CTGGCTCCTTTTAAATGCATTAGCTGGTTTTATGAGCCT------GTTTTTCAGTGTTGTAATTTTTTAATACGCGCTGTGATGAAC-----------------------------------TAGTTCAACTTCCGCTGAT ; END; BEGIN TREES; Title 'Trees from "Fibrodontia & allied fungi ITS Bayesian analysis.tre"'; LINK Taxa = Taxa; TRANSLATE 1 Hyphodontia_subalutacea_DQ340341, 2 Hyphodontia_floccosa_DQ873618, 3 Fibrodontia_alba_KC928274, 4 Fibrodontia_alba_JQ612713, 5 Fibrodontia_gossypina_DQ249274, 6 Fibrodontia_brevidens_KC928276, 7 Trechispora_farinacea_EU909231, 8 Subulicystidium_longisporum_JQ905612, 9 Porpomyces_mucidus_FJ496660, 10 Sistotremastrum_suecicum_EU118666; TREE con_50_majrule = (1:0.0786697893882918,2:0.1235432506429197,((((((3:0.01008107412242461,4:0.01036737860828542):0.015289291691521,5:0.0581864316147282):0.02845261351475778,6:0.02864379139440228):0.1302472112366548,7:0.2438876366042929,9:0.2080926391470768):0.1278675518360091,10:0.3652422979557832):0.06628456079251628,8:0.2270293718846477):0.1410927842689555); END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 585; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 585; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 585; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1371903009729; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 6754418626036687649; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 5834906486675691696; mqVersion 275; checksumv 0 3 579972272 null getNumChars 585 numChars 585 getNumTaxa 10 numTaxa 10 short true bits 15 states 15 sumSquaresStatesOnly 104249.0 sumSquares 104249.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 287; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1060 562; setLocation 136 19; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #6754418626036687649 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #6754418626036687649; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; getTable; tell It; rowNamesWidth 206; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 773 495; setLocation 136 19; 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.ManageTrees.ManageTrees; tell It; showTrees 0 #mesquite.lists.TreesList.TreesList; tell It; setTreeBlock 1; getWindow; tell It; newAssistant #mesquite.lists.NumForTreeList.NumForTreeList; tell It; suppress; setValueTask #mesquite.trees.NumberOfTaxa.NumberOfTaxa; desuppress; endTell; newAssistant #mesquite.lists.TreeListRooted.TreeListRooted; newAssistant #mesquite.lists.TreeListPolys.TreeListPolys; newAssistant #mesquite.lists.TreeListPolyAssumption.TreeListPolyAssumption; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 773 495; setLocation 136 19; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; endTell; showWindow; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #6754418626036687649 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1484.1371899137429.5117998320785517086; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 773 495; setLocation 136 19; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.coalesce.LineageWidth.WidthsToolExtra.LineageWidth; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle on; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; 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 on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; 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 on; 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 #5834906486675691696 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 221; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 773 495; setLocation 136 19; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; 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; 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; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; showCharacters #5834906486675691696 #mesquite.lists.CharacterList.CharacterList; tell It; setData 0; getWindow; tell It; newAssistant #mesquite.lists.CharListInclusion.CharListInclusion; newAssistant #mesquite.stochchar.CharListProbModels.CharListProbModels; newAssistant #mesquite.lists.CharListCodonPos.CharListCodonPos; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 773 495; setLocation 136 19; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; endTell; showWindow; getEmployee #mesquite.lists.CharListAnnotPanel.CharListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; endTell; end;