#NEXUS [written Thu Aug 21 00:13:37 EDT 2014 by Mesquite version 2.75 (build 564) at owner-PC/10.0.0.5] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=40; TAXLABELS Kendrickiella_phycomyces_AB671461 Cadophora_finlandica_AF486119 Mycelium_radicis_atrovirens_AF486120 Phialocephala_dimorphospora_AF486121 Phialocephala_fusca_AF486122 Sporendocladia_bactrospora_AF486123 Phialocephala_fluminis_AF486124 Phialocephala_compacta_AF486125 Phialocephala_scopiformis_AF486126 Phialocephala_xalapensis_AF486128 Sporendocladia_bactrospora_AF486130 Phialocephala_humicola_AF486131 Phialocephala_virens_AF486132 Leptodontidium_orchidicola_AF486133 Phialocephala_turiciensis_AY078128 Phialocephala_turiciensis_AY078129 Phialocephala_letzii_AY078130 Phialocephala_cf._fortinii_AY078131 Phialocephala_cf._fortinii_AY078132 Phialocephala_europaea_AY078133 Phialocephala_fortinii_AY078134 Phialocephala_helvetica_AY078136 Phialocephala_europaea_AY078137 Phialocephala_fortinii_AY078138 Phialocephala_fortinii_AY078140 Phialocephala_fortinii_AY078141 Phialocephala_helvetica_AY078142 Phialocephala_fortinii_AY078143 Phialocephala_fortinii_AY078144 Acephala_applanata_AY078145 Acephala_applanata_AY078146 Acephala_applanata_AY078147 Acephala_applanata_AY078148 Acephala_applanata_AY078149 Acephala_applanata_AY078150 Acephala_applanata_AY078151 Phialocephala_cf._fortinii_AY078152 Sclerotinia_sclerotiorum_NW001820801 Phialocephala_fortinii_PPE528S Phialocephala_podophyllae_PPE728S ; END; BEGIN CHARACTERS; TITLE PPE5&7_28S_alignment; DIMENSIONS NCHAR=99; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Kendrickiella_phycomyces_AB671461 ????????????????????????????????????????CBADADBAADAACBCCACCA??????????????????????????????????????? Cadophora_finlandica_AF486119 CCDDCABBDBCCADBACCDACCCADABBBCBDCAA???????????????????????????????????????????????????????????????? Mycelium_radicis_atrovirens_AF486120 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_dimorphospora_AF486121 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_fusca_AF486122 CCDDCABBDBCCADBACBDA??????????????????????????????????????????????????????????????????????????????? Sporendocladia_bactrospora_AF486123 ???????????????????????????????????????CCDDCABBDBCAADBACCDACCA????????????????????????????????????? Phialocephala_fluminis_AF486124 CCDDCABBDBCCADBACCDACCAADABBBCBDCAABDDAACBADADBAADAA??????????????????????????????????????????????? Phialocephala_compacta_AF486125 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_scopiformis_AF486126 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_xalapensis_AF486128 ???????????????????????????????????????CCDDCABBDBCAADBACCDACCAADABBBCBDCAABDDAACBADADBAADAACBCCACCA Sporendocladia_bactrospora_AF486130 ???????????????????????????????????????CCDDCABBDBCAADBACCDACCACCABBBCBDCAABDDAACBADADBAADAACBCCACCA Phialocephala_humicola_AF486131 CCDDCABBDBCAADBACCDACCAADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_virens_AF486132 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Leptodontidium_orchidicola_AF486133 CCDDCABBDBCCADBAACDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_turiciensis_AY078128 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_turiciensis_AY078129 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_letzii_AY078130 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_cf._fortinii_AY078131 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_cf._fortinii_AY078132 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_europaea_AY078133 CCDDCABBDBCCADBACCDACCCA??????????????????????????????????????????????????????????????????????????? Phialocephala_fortinii_AY078134 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_helvetica_AY078136 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_europaea_AY078137 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_fortinii_AY078138 CCDDCABBDBCCADBAACDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_fortinii_AY078140 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_fortinii_AY078141 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_helvetica_AY078142 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_fortinii_AY078143 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_fortinii_AY078144 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Acephala_applanata_AY078145 CCDDCABBDBCCADBACCDACCCADABBBCDDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Acephala_applanata_AY078146 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Acephala_applanata_AY078147 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Acephala_applanata_AY078148 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Acephala_applanata_AY078149 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Acephala_applanata_AY078150 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Acephala_applanata_AY078151 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_cf._fortinii_AY078152 CCDDCABBDBCCADBAACDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Sclerotinia_sclerotiorum_NW001820801 CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_fortinii_PPE528S CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? Phialocephala_podophyllae_PPE728S CCDDCABBDBCCADBACCDACCCADABBBCBDCAABDDAACBADADBAADAACBCCACCA??????????????????????????????????????? ; END; BEGIN TREES; Title '8SMEGA-MLBS1000consensus'; LINK Taxa = Taxa; TRANSLATE 1 Kendrickiella_phycomyces_AB671461, 2 Cadophora_finlandica_AF486119, 3 Mycelium_radicis_atrovirens_AF486120, 4 Phialocephala_dimorphospora_AF486121, 5 Phialocephala_fusca_AF486122, 6 Sporendocladia_bactrospora_AF486123, 7 Phialocephala_fluminis_AF486124, 8 Phialocephala_compacta_AF486125, 9 Phialocephala_scopiformis_AF486126, 10 Phialocephala_xalapensis_AF486128, 11 Sporendocladia_bactrospora_AF486130, 12 Phialocephala_humicola_AF486131, 13 Phialocephala_virens_AF486132, 14 Leptodontidium_orchidicola_AF486133, 15 Phialocephala_turiciensis_AY078128, 16 Phialocephala_turiciensis_AY078129, 17 Phialocephala_letzii_AY078130, 18 Phialocephala_cf._fortinii_AY078131, 19 Phialocephala_cf._fortinii_AY078132, 20 Phialocephala_europaea_AY078133, 21 Phialocephala_fortinii_AY078134, 22 Phialocephala_helvetica_AY078136, 23 Phialocephala_europaea_AY078137, 24 Phialocephala_fortinii_AY078138, 25 Phialocephala_fortinii_AY078140, 26 Phialocephala_fortinii_AY078141, 27 Phialocephala_helvetica_AY078142, 28 Phialocephala_fortinii_AY078143, 29 Phialocephala_fortinii_AY078144, 30 Acephala_applanata_AY078145, 31 Acephala_applanata_AY078146, 32 Acephala_applanata_AY078147, 33 Acephala_applanata_AY078148, 34 Acephala_applanata_AY078149, 35 Acephala_applanata_AY078150, 36 Acephala_applanata_AY078151, 37 Phialocephala_cf._fortinii_AY078152, 38 Sclerotinia_sclerotiorum_NW001820801, 39 Phialocephala_fortinii_PPE528S, 40 Phialocephala_podophyllae_PPE728S; TREE PPE5&7_28S_tree = (38:1.0,(18:1.0,((21:1.0,27:1.0):1.0,(((26:1.0,34:1.0):1.0,((9:1.0,36:1.0):1.0,(((19:1.0,28:1.0):1.0,(33:1.0,39:1.0):1.0):1.0,((35:1.0,40:1.0):1.0,((13:1.0,17:1.0):1.0,((15:1.0,31:1.0):1.0,(16:1.0,29:1.0):1.0):1.0):1.0):1.0):1.0):1.0):1.0,(((8:1.0,25:1.0):1.0,(22:1.0,23:1.0):1.0):1.0,((3:1.0,4:1.0):1.0,(32:1.0,(2:1.0,((20:1.0,30:1.0):1.0,((37:1.0,(14:1.0,24:1.0):1.0):1.0,((1:1.0,(7:1.0,12:1.0):1.0):1.0,(5:1.0,(10:1.0,(6:1.0,11:1.0):1.0):1.0):1.0):1.0):1.0):1.0):1.0):1.0):1.0):1.0):1.0):1.0):1.0); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 99; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 99; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 99; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1408594417458; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 1729490905514387466; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 1492952760913861950; mqVersion 275; checksumv 0 3 3894791992 null getNumChars 99 numChars 99 getNumTaxa 40 numTaxa 40 short true bits 2305843009213693967 states 15 sumSquaresStatesOnly 165141.0 sumSquares -2.0245301620896233E21 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 282; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 969 635; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #1729490905514387466 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 2878.1408540009608.2375358859099977684; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 687 568; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow; 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 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 #1492952760913861950 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 318; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 687 568; setLocation 8 22; setFont SanSerif; setFontSize 10; 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; 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;