#NEXUS [written Thu Oct 01 12:42:11 MSK 2015 by Mesquite version 2.73 (build 544) at Vera-Kate/94.19.95.218] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=15; TAXLABELS Sporidiobolus_johnsonii_AF444509_ Filobasidium_capsuligenum_EF611232 Sistotrema_sernanderi_AY805624_ Hydnum_repandum_JX093561 Rogersiomyces_malaysianus_KT779284 Rogersiomyces_malaysianus_KT779285 Ceratobasidium_cornigerum_EU273525 Thanatephorus_cucumeris_EU244843 Sistotremastrum_guttuliferum_JX310445 Haplotrichum_conspersum_DQ911612 'Auricularia auricula-judae KJ698425' Cryptococcus_neoformans_FJ914894 Sistotrema_confluens_KC862587 Craterellus_cornucopioides_JF907967 Cantharellus_cibarius_KJ184345 ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=446; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Sporidiobolus_johnsonii_AF444509_ cgtaggtgatcatgagggtgtcaattgaccttctcacttctaaccctgtgcatcttatggtctgctttgcgagccttcacttaaacaccagtctagaatgtatataatctatataaaaactttcaacaacggatctcttggctctcgcatcgatgaagaacgcagcgaaatgcgatacgtaatgtgaattgcagaattcagtgaatcatcgaatctttgaacgcatcttgcactctctggtattccggagagtatgtctgttggagtgtcatgaattcttcaaccccaccgtttcttgaagccgtgtgcttggattctgagcgtgctgattattagctcgttcgtaatgcattagcatcccgatgaaagtttggattgacttggcgtaatagactattcgctaaggacactagccaacttcaaagcttctaatcaagtctgatcaa Filobasidium_capsuligenum_EF611232 caca----------------------------------tccacacctgtgaactgtaagatgtgtttcgcggcatctgccataaacaataatgtcaaatgtattataa--tcaataaaactttcaacaacggatctcttggctctcgcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattcagtgaatcatcgaatctttgaacgcaccttgcgctccttggtattccgaggagcatgcctgtttgagtgtcatgaaaatatcaaccaagacttgggtttctctgttcggcttggaattgggtgctgcaatcagatggctcaccttaaaagaattagctggatctgtttagattggtttgacttggcgtaataagtatttcgctaaggaggatggccaataacgccgcttctaatctttcctgacaaa Sistotrema_sernanderi_AY805624_ tg----------------agctaattgctctctcatcctttacacctgtgcactttgaggggacttttactccccttcaactatacacttattacgaatgcgcttaactttaaatacaacttttaacaacggatctcttggctctcgcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattcagtgaatcatcgaatctttgaacgcaccttgcgctccctggtattccggggagcacgcctgttcgagcgtcatgaagctctcaaatagcctcttttcttgcaagatgtgtttggatttggactctgctgtgaaacagctggtccgaaagatattagctgatcc-tagcagattggttctactcggcgtgataattatctcgttgaggaagatggccaaaactattgcttctaatcgtcttcgacgaa Hydnum_repandum_JX093561 cgtaggtgatcagggggttgccagttactcttctgatttttacacctgtgcacttttcaaagagggtagctgcctttggaacaaccccctgtattgaatgtgccacaattttaatacaacttttaacaacggatctcttggctctcgcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattcagtgaatcatcgaatctttgaacgcatcttgcgctctctggtattccggggagcacatctgttcgagtgtcatgaaactctcaaataaaggtggattttctatcatctgtttggatttggactttgctgcaatgtggctagtcttaaatgtattagcttggtcctcatggtttggttctactcggcatgataattatcttgttgaggagactggccatgtctcttgcttctaaattgtcttgacgaa Rogersiomyces_malaysianus_KT779284 cattaatgattgccagcatgccgttcacaattctatcctatacacctgtgcactctgaaggggtctctgctatctccttcttaaactctgatttcgaatgcgccgaaaatcttatacaacttttaacaacggatctcttggctctcgcatcgatgaagaacgcagcgaattgcgataagtaatgtgaattgcagaattcagtgaatcatcgaatctttgaacgcaccttgcgctccctggtattccggggagcacgcctgttcgagtgtcgtgaagtcctcaagccaggatggtttttgaacgtccggcttggatttggactctggcttgcaacggctggtcttaaaagcattagctggtccatgttactatggttctactcggcgtgataagtctctcgctgaggaatgtagatggccgtgccgcttctaatcttgcctggcaaa Rogersiomyces_malaysianus_KT779285 cattaatgattgctagcatgccgttcacaattctatcctatacacctgtgcactctgaaggggtct?tgctatctccttcttaaactctgatttcgaatgcgccgaaaatcttatacaacttttaacaacggatctcttggctctcgcatcgatgaagaacgcagcgaattgcgataagtaatgtgaattgcagaattcagtgaatcatcgaatctttgaacgcaccttgcgctccctggtattccggggagcacgcctgttcgagtgtcgtgaagtcctcaagccaggatggtttttgaacgtccggcttggatttggactctggcttgcaacggctggtcttaaaagcattagctggtccatgttactatggttctactcggcgtgataagtctctcgctgaggaatgtagatggccgtgccgcttctaatcttgcctggcaaa Ceratobasidium_cornigerum_EU273525 cgtaggtgatcaagaggttgcccctcgcct-tctcttttccacacctgtgcactttgagacggacttttcttccgtctacttactcattaattatgaatgtgatgtaaattagaactaagtttcaacaacggatctcttggctctcgcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattcagtgaatcatcgaatctttgaacgcaccttgcgctccttggtattccttggagcatgcctgtttgagtatcatgaaattctcaaagtaaatcttttgttcaatggttgctttggacttggaggttgcagatcgtctgctcctcttaaatgcattagctggatctcagtatgttggttccactcggcgtgataagtatcacgctgaggaaagtggccaagtacaccgcttctaatagtctatgacaaa Thanatephorus_cucumeris_EU244843 ggtaggtgatcaataggttgcctcatacctatctcttttccacacctgtgcactttgaggcttgttttaactctgtctactcactcaattattttgaatgggatgtaatctaatactaagtttcaacaacggatctcttggctctcgcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattcagtgaatcatcgaatctttgaacgcaccttgcgctccttggtattccttggagcatgcctgtttgagtatcatgaaatcttcaaagtaaatcttttgttcaatggttactttggtattggaggttgcagctcacctgctcctctt--gttcattagctggatctcagtatgttggttccactcagcgtgataagtatctcgctgaggaaggtggccaagtgcaccgcttctaatagtccatgac--a Sistotremastrum_guttuliferum_JX310445 caaagttgcttacagcgttgtcggtcaggtagctcttgttcacccctgtgcacctagaggggagcgcgtcgacgttgccctcaaaatcttgtctagaatgtctgataaaaacaaaataactttcaacaacggatctcttggctctcgcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattcagtgaatcatcgaatctttgaacgcaccttgcgctccttggtattccgaggagcatgcctgtttgagtgtcatgataatctcaaatcaacattttagtttaattgttgacttggacttggaggttgctgattattggctcctcttaaatgcattagctggattactatagtatagtcca---tggtgttgtaatctcggcgctgtgacaactatacaat----ctgcttctaaaattgcctaataaa Haplotrichum_conspersum_DQ911612 ggtgtgccgccccgcgcacgccgcctgcagtccaacctctcacacccgtgcacaccgtcgggcgctccgc-----cccgaccttccacaagccacgaaagtgcgcttgccgaaaaacaacttttaacaacggatctcttggttctcgcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattcagtgaatcatcgaatctttgaacgcaccttgcgctccttggtattccgaggagcatgcccgtttgagtgtctcgatatcatcaggcgcccgtgcccttgcggcggtgcgactggacttggacgttgccggggcccggctcgtcttaaatgcattagcgagagacgctatctccggctctcattggcgtgataaggtcaccgtcgagagcggtcacgagctgcgccgcttctaaccgtccctgacgga 'Auricularia auricula-judae KJ698425' tgggggtcttcattcagctgtcgcttgctggacgaaaactcacacctgtgcacctcggtgcggtttcggccgcttccgctttaactacaagtccagaatgtgatctaaaaaagtaacaactttcaacaacggatctcttggctctcgcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattcagtgaatcatcgaatctttgaacgcaccttgcgctccttggtattccatggagcatgcctgtttgagtgtcacgtaaaccctcacccgtcgcccgc-------------ggtggacttggaccgtgccgt-aatcggctcgtcttgaatgcattagctggcgcttttaagtctgggcga---cggtgtgataattatctcgccaataggggccttcagcggcgctgcttacagccgtccctgacaaa Cryptococcus_neoformans_FJ914894 cgtaggtgatcagtagagaatgacttatttatctaccctctacacctgtgaactgttatgtgctt----cggcacgttttacaaacttcaatgttgaatgtattataacaataataaaactttcaacaacggatctcttggcttccacatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattcagtgaatcatcgagtctttgaacgcaacttgcgccctttggtattccgaagggcatgcctgtttgagagtcatgaaaatctcaatccctcgggttttattaccgttggacttggatttgggtgttgccgcgcgtcggctcgccttaaatgtgttagtgggaaggtgata---cctgtcagcccggcgtaataag--tttcgctgggccgggtagtcttccttgctg-------------ataacaaa Sistotrema_confluens_KC862587 cgtaggtgatcatagggttacgacttagcttaatattttctacacctgtgcattgtctatctaaa---------------atagatttagacgtcgaatgcct--caatatgtatacaacttttaacaacggatctcttggttctcgcatcgatgaagaacgcagcgaaatgcgataggtaatgtgaattgcagaattcagtgaatcatcgagtctttgaacgcaccttgcgctccctggtactccggggagcacgtctgttcgagtgtcctaaagaccatcagacataggtgccacttacc--tatgtctggagctggaccttgctgt-aaatggctggtctgaaacacattcgtgggtacgttata---gcagtcctccgggcgtgatatctaatcaacaacgaaaactgtctaactggactgcttctaatg------gctgaa Craterellus_cornucopioides_JF907967 aaggcttgtttgtcagactgtgagtaagttgttggtcattgaaagcaatccactctggggagggtttgactgtattctatct-ctctctagtctcgagtgtatcataactcatttacaactttcagcaatggatctcttggttctcgcatcgatgaagaacgcagtgaaatgcgataactggtgtgaattgcaacaccaagtgaatcatcgagtctttgaacgca-attgcgccctctggtattggagggggtacgtctgttcgagggtcatttgaacctctcaaagggtttttggcttaa-aaaccctttggatttgggtcttgccgtgtcttggctcaccttgaaagcattagcaagtctttttggaggcgttgtaatttggtcagg------cctccttgagaggattcgtctcaaaaattgcttccaatggcccctggc--- Cantharellus_cibarius_KJ184345 cgtgcgctcttctggggtctccggtggccgttccagttcccaggcatgtccagtcccctggggccttggcggctgccccggcattccggggcctcaaatgtccaatggtttatagataactctca?caatggatctctaggctcttgcatcgatgaagaacgcagtgaactgcgataactggtgtgaattgcaacaccaagcgaatcatcgagtctttgaacgcaaacggcacccttcagtgtggccaagggtatctctggctgagggtaatgggaacttgatccag------tgtaaccgtggttagctggggattgggctttggggtactctggcttgccttaaatgcattggctggcccttgacatagtgctttttttcagtctagccaaaaggctggtgaaggacttgggctgcggcgcagc-tctgttcgcgtccgtcgca ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 446; END; BEGIN TREES; Title 'Trees from "ITS.tre"'; LINK Taxa = Taxa; TRANSLATE 1 Sporidiobolus_johnsonii_AF444509_, 2 Filobasidium_capsuligenum_EF611232, 3 Sistotrema_sernanderi_AY805624_, 4 Hydnum_repandum_JX093561, 5 Rogersiomyces_malaysianus_KT779284, 6 Rogersiomyces_malaysianus_KT779285, 7 Ceratobasidium_cornigerum_EU273525, 8 Thanatephorus_cucumeris_EU244843, 9 Sistotremastrum_guttuliferum_JX310445, 10 Haplotrichum_conspersum_DQ911612, 11 'Auricularia auricula-judae KJ698425', 12 Cryptococcus_neoformans_FJ914894, 13 Sistotrema_confluens_KC862587, 14 Craterellus_cornucopioides_JF907967, 15 Cantharellus_cibarius_KJ184345; TREE tree_1 = (1:0.234911975,(9:0.34313186,((7:0.03141858,8:0.08905772):0.16540203,((10:0.45319789,11:0.31731851):0.21588324,(((2:0.16635274,12:0.39005401):0.09075484,(14:0.51106681,15:1.1247718):0.59142723):0.03673715,((5:0.00267746,6:1.13E-6):0.27005864,(13:0.59634159,(3:0.20391142,4:0.25653717):0.06955697):7.101E-5):0.09684746):0.01187873):0.03399469):0.06335992):0.234911975)[% ] [% ] [% setBetweenBits = selected ]; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 446; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 446; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1443692531320; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8109406677963584155; tell It; attachments ; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 5088474495217455255; mqVersion 273; checksumv 0 2 3486767693 null getNumChars 446 numChars 446 getNumTaxa 15 numTaxa 15 short true bits 1152921504606846991 states 15 sumSquaresStatesOnly 155619.0 sumSquares -3.548692391179875E21 NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 264; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 873 1082; setLocation 188 9; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #8109406677963584155 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #8109406677963584155; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; getTable; tell It; rowNamesWidth 203; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 609 1015; setLocation 188 9; 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 609 1015; setLocation 188 9; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; endTell; showWindow; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #8109406677963584155 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1038.1443691965450.6576508277871851938; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 609 1015; setLocation 188 9; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.reroot; 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; 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 #5088474495217455255 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 609 1015; setLocation 188 9; 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; 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;