#NEXUS [written Sun Nov 19 19:01:31 EET 2017 by Mesquite version 3.31 (build 859) at MacBook-Air.local/192.168.0.11] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=11; TAXLABELS Saccoloma_inaequale Lindsaea_digitata Lindsaea_quadrangularis Lindsaea_sagittata Nesolindsaea_kirkii Lindsaea_ensifolia Odontosoria_chinensis Lindsaea_sp2 xLindsaeosoria_flynnii_a xLindsaeosoria_flynnii_b xLindsaeosoria_flynnii_c ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=809; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Saccoloma_inaequale gcaggcactagggagcaaagaggggacaacggtatgatgtttctggatgctgttgcccccaatggccctttgaatctgaactcaaaggagcatgctcaacaagagcacagtcatgcacagtttgggcctccggggcttctggctttaccagaaccgagtagtgacaatgagggacgaaaactagcaagaaagaaacaaaagcgaaggctgtctcga?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????-------------------------------- Lindsaea_digitata ??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????gacaatgagggccggaaactagccagaaagaaacaaaagcgcaggctgtcacgagagcccggtgaggatggggatgacaggacaagggagcatcccttcatagtgacagagccaggcgaagtggccagggggaagaagaatggcttagattacctgtttgatctctacgagcagtgtgcaaggttcctagatgaagtgcagcagatctcaagggaaaggggggaaaaatgccctacgaaggtataacactggtaatgcccaaattgtgttgaagagagagagttctttagttacattg------aagactaagactaaagtgttctcta--tgtgcaaattgctctgtatatgtacgtgtgtgtgcgtgtttgggccgtagtagaaggtttctccatgtggccaataataaatatcatctttatgttgcatttgaaaggtgtgcctgaatcagtttcttgtttggatatc-------tccgag--ttatgtttatcgtacttgttgttaagcctcgttccttgctgcaggtgacgaatcaagtgtttcgacatgccaagcttaaaggagccagctacatcaacaaaccaaagatgcggcattatgtccattgctttgctctgcactgcctggacaaggagaaatcca Lindsaea_quadrangularis ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????gaagtggccagggggaagaagaatggcttagattacctgtttgatctctacgagcagtgtgcaaggttcctagatgaagtgcagcagatctcaagggaaaggggggaaaaatgccctacgaaggtataacactggtaatgcccaaattgtgttgaagagagagagttctttagttacattg-------agactaagactaaagtgttctcta--tgtgcaaattgctctgtatatgtacgtgtgtgtgcgtgtttgggccatagtagaaggtttctccatgtggccaataataaatatcatctttatgttgcatttgaaaggtgtgcctgaatcagtttcttgtttggatatcagaaccttccgag--ttatgtttatcgtacttgttgttaagcctcgttccttgctgcaggtgacgaatcaagtgtttcgacatgccaagcttaaaggagccagctacatcaacaaaccaaagatgcggcattatgtccattgctttgctctgcactgcctggacaaggagaaatcca Lindsaea_sagittata ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????gcatcccttcatagtgacggagccaggcgaagtggccagggggaagaagaatggcttagattacctgtttgatctctacgagcagtgtgcaaggttcctagatgaagtgcagcagatctcaagggaaaggggggaaaagtgccctacgaaggtataacactggtaatgcccaaattgtgttgaagagagagagttctttagttacattg------aagactaagactaaagtgttctcta--tgtgcaaattgctttgtatatgtacgcatgtgtgcgtgtttgggccatagtagaaggtttctccatgtggctgataataaatatcatctttatgttgcatttgaaaggtgtgcctgaatcagtttcttgtttggatatcagaaccttccgag--ttatgtttatcatacttgttattaagcctcgttccttgctgcaggtgacgaatcaagtgtttcgacatgccaagcttaaaggagccagctacatcaacaaaccaaagatgcggcattatgtccattgctttgctctgcactgcctggacaaggagaaatcca Nesolindsaea_kirkii gcaggaactagggagcaaagaggggacaatggtatgatgttccctgatgctattgccctgggtgaccctctgaatctgaactcaagggagcatgcacaacaagagcatagccatgtgcagtttggtgtgccaggtaatttggctttgccagagccgagtagtgacaatgagggacaaaaactagccagaaagaaacaaaagcggaggctgtcgagagagccaggtgaggatggggatgacagRacMagggagcatcccttcatagtaacggagccgggtgaagtggcaagggggaagaagaatggcttagattacctStttgatctctaYgagcagtgtgcaaggttcctagaKgaagtgcagcagatctctagagMaaggggggaaaaRtgccctacgaaggtataatactggtagtgccca?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? Lindsaea_ensifolia ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????cagagagagttctttagttacattg------aagactaagacgaaagtgttctcta--tgtgcaaattgatttgtatatgcacgcgtgtgtgcatgtttgggccatagtagaaggtttctccttgtggccgataataaatatcatctttaagttgcatttgaaaggtgtgcctgaatcagtttcttgtttggatatccagaac-tgtcag--ttatgtttatcgtgcttgttgttaagccttgttccttgctgcaggtgacgaatcaagtgtttcgacatgccaagcttaaaggtgccagctacatcaacaaaccaaagatgcggc???????????????????????????????????????????????? Odontosoria_chinensis ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ccagagccaagtagtgacaatgagggccggaaactagcgagaaagaaacaaaagcggaggctgtcacgagagcctggtgatgatggggatgacaggacaagggagcatcccttcatagtgacggagccaggtgaagtggcaagggggaagaagaatggcttagattacctgtttgatctctacgagcagtgtgcaaggttcctagatgaagtgcagcagatctcaagagaaaggggggaaaaatgccctacgaaggtataatgctggtaatgcccaatttgtattg--aagagagagttttttaactacatgtaaaaataaaaataaaacaaaggtgctctctaattgtgaaaagtgct-tgtatatgtactcgcctgtgtgtggttaggctttcatagaagggttctccatgtgctcaataaaaagtattgtctttctggtgtatttaataggtgt--cctaattagtttcttgctcaaattttgcagaatttccagatttatgtttgtcttacttgttgttaacc-----------ctgcaggtaacgaatcaagtgtttcgacatgccaagcttaaaggtgccagctacatcaacaaaccaaagatgcggcattatgtccattgctatgctctgcactgcctggacaaggagaagtcca Lindsaea_sp2 gcaggaactagggagcaaagaggggataatggtataatgtttcctgatgctgttgctctgggtgaccctttgaatctgaactcaagggagcatgtgcaacaagagcatagtcatgctcagtttggtccaccaggtaatctggctttaccagagccaagtagtgacaatgagggccggaaactagccagaaagaaacaaaagcgcaggctgtcacgagagccaggtgaggatggggatgacaggacaagggagcatcccttcatagtgacagaaccaggcgaagtggccagggggaagaagaatggcttagattacctgtttgatctctacgagcagtgtgcaaggttcctagatgaagtgcagcagatctcaagggaaaggggggaaaaatgccctacgaaggtataacactggtaatgcccaaattgtgttgaagagagagagttctttagttacattga-----agacttaagacgaaagtgttctcta--tgtgcaaattgctttgtatatgtac--gtgtgtgcatgtttgggctatagtagaaggtttctctatgtggccgataataaatatcatcttcacgttgcattggaaaggt??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? xLindsaeosoria_flynnii_a ??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????GAGCAGTGTGCAAGGTTCCTAGATGAAGTGCAGCAGATCTCAAGGGAAAGGGGGGAAAAATGCCCTACGAAGGTATAACACTGGTAATGCCCAAAT??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????TTCTTGTTTGGATATCCAGAAC-TGTCAG--TTATGTTTATCGTGCTTGTTGTTAAGCCTTGTTCCTTGCTGCAGGTGACGAATCAAGTGTTTCGACAT?????????????????????????????????????????????????????????????????????????????????????????????? xLindsaeosoria_flynnii_b ??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????GAGCAGTGTGCAAGGTTCCTAGATGAAGTGCAGCAGATCTCAAGGGAAAGGGGGGAAAAATGCCCTACGAAGGTATAACACTGGTAATGCCCAAAT??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????TTCTTGTTTGGATATCCAGAAC-TGTCAG--TTATGTTTATCGTGCTTGTTGTTAAGCCTCGTTCCTTGCTGCAGGTGACGAATCAAGTGTTTCGACAT?????????????????????????????????????????????????????????????????????????????????????????????? xLindsaeosoria_flynnii_c ??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????GAGCAGTGTGCAAGGTTCCTAGATGAAGTGCAGCAGATCTCAAGAGAAAGGGGGGAAAAATGCCCTACGAAGGTATAATGCTGGTAATGCCCAATT??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????TAATTAGTTTCTTGCTCAAATTTTGCAGAATTTCCAGATTTATGTTTGTCTTACTTGTTGTTAACC-----------CTGCAGGTAACGAATCAAGTGTTTCGACAT?????????????????????????????????????????????????????????????????????????????????????????????? ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 809; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 809; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 809; END; BEGIN TREES; Title 'Trees from "analysis.con.tre"'; ID 015fd53a16703; LINK Taxa = Taxa; TRANSLATE [0] 1 Saccoloma_inaequale, [1] 2 Lindsaea_digitata, [2] 3 Lindsaea_quadrangularis, [3] 4 Lindsaea_sagittata, [4] 5 Nesolindsaea_kirkii, [5] 6 Lindsaea_ensifolia, [6] 7 Odontosoria_chinensis, [7] 8 Lindsaea_sp2, [8] 9 xLindsaeosoria_flynnii_a, [9] 10 xLindsaeosoria_flynnii_b, [10] 11 xLindsaeosoria_flynnii_c; TREE con_50_majrule = (1:0.442972,(7:0.01289255,11:0.01191618):0.1693511,((((2:0.01060193,3:0.004594361):0.02226472,4:0.04114519):0.03867647,((6:0.01292284,9:0.01220366):0.02132333,10:0.01446887):0.07465885,8:0.08344351):0.2061961,5:0.1871527):0.2552506); END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1511110891993; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8852533262142698993; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 2371122019009339882; mqVersion 331; checksumv 0 3 4270182353 null getNumChars 809 numChars 809 getNumTaxa 11 numTaxa 11 short true bits 3458764513820540943 states 15 sumSquaresStatesOnly 99547.0 sumSquares -3.85767535441451E21 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 700 464; setLocation 8 23; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #8852533262142698993 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; setTreeBlockID 015fd53a16703; toggleUseWeights off; endTell; setAssignedID 1177.1511110881930.2391093962034863388; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 600 392; setLocation 8 23; 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; toggleShow consensusFrequency; toggleShow bootstrapFrequency; toggleShow posteriorProbability; toggleShow consensusFrequency; toggleShow posteriorProbability; toggleShow bootstrapFrequency; setDigits 4; setThreshold ?; writeAsPercentage off; toggleCentred off; toggleHorizontal on; toggleWhiteEdges on; toggleShowOnTerminals 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; toggleShowOnTerminals on; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #2371122019009339882 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 600 392; setLocation 8 23; 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.AlterData.AlterData; tell It; toggleBySubmenus off; 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 16 6 1 1; 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;