#NEXUS [written Thu Sep 24 17:58:57 JST 2020 by Mesquite version 3.61 (build 927) at tsutsumichie-no-iMac.local/202.220.64.189] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=12; TAXLABELS Osmunda_regalis_R10 Osmunda_japonica_J1J2J3J4J5J6J7J8 Osmunda_regalis_R15 Osmunda_regalis_R13aR14a Osmunda_regalis_R14b Osmunda_regalis_R13bR17R18 Osmunda_lancea_L1L2L3 Osmunda_regalis_R5R6R7R8R9 Osmunda_regalis_R1R2R3R4 Osmunda_regalis_R111R12 Osmunda_regalis_R16 Claytosmunda_claytoniana_CL2 ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=559; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Osmunda_regalis_R10 TCAGATTGTCGCCTTTGAATCCCAGACCATCAAGAACATGATCGAAGACACTGGCTGTGATGCCCCTATTCCCCTCCCTAACGTTTCCAGCAAGATCCTTGCCAAGGTCATTGAATTTTGTAAGTTCCATGTCAACTCTAAGAAGACTGGCGATGATGGTTGCGGTCCCTCCGAGGAGGAAGTTAAGTCCTTCGACGCTGAATTCGTGAAAGTTGATCAGCAAACGCTCTTCGACCTCATCCTGGTATGTTT------------------CTTGGTCTTCTTGTTTCTTGCTTGAGCATGATCTTTCGTTGCCTTTGTACATTCTTTTCAAATCTTTTGCTCAGCCGTTGTTGTTCCATGCGTTAAAGTCTGTAGATTCGGGAGTCTTTGCTGACTTTCCCCTT-CTATTGTTATGCACAGGCAGCAAATTACCTCAACATCATGAATCTGTTGGATCTGACCTGCCAGACCGTGGCAGACATGATCAAAGGCAAGACGCCAGAGGAGATTCGCAGTACTTTCAACATCAAGAACGATTTTACTCCAGAAGAAGAGGAA Osmunda_japonica_J1J2J3J4J5J6J7J8 TCAGATTGTCGCCTTTGAATCCCAGACCATCAAGAACATGATCGAAGACACTGGCTGTGATGCCCCTATTCCCCTCCCTAACGTTTCCAGCAAGATCCTTGCCAAGGTCATTGAATTTTGTAAGTTCCATGTCAACTCTAAGAAGACTGGTGATGATGGTTGCGGTCCCTCCGAGGAGGAAGTCAAGTCCTTCGACGCTGAATTCGTGAAAGTTGATCAGCAAACCCTCTTCGACCTCATCCTGGTATGTTT------------------CTTGGTCTTCTTGTTTCTTGCTTGAGCATGATCTTTCGTTGCCTTTGTACATTCTTTTCAAATCTTTTGCTCAGCCGTTGTTGTTCCATGTTTTAAAGTTTGTAGATTCGGGAGTCTTTGCTGACTTTCCCCTT-CTATTGTTATGCACAGGCGGCAAATTACCTCAACATCATGAATCTTTTGGATCTGACCTGCCAGACCGTGGCAGACATGATCAAAGGCAAGACGCCAGAGGAGATTCGTAGTACTTTCAACATCAAGAACGATTTTACTCCAGAGGAAGAGGAA Osmunda_regalis_R15 TCAGACTGTCGCCTTTGAATCCCAGACCATCAAGAACATGATCGAAGACACTGGCTGTGATTCCCCTATTCCCCTCCCTAACGTTTCCAGCAAGATCCTTGCCAAGGTCATTGAATTTTGTAAGTTCCATGTCAACTCTAAGAAGACTGGTGATGATGGTTGCGGTCCCTCCGAGGAGGAAGTCAAGTCCTTCGACGCTGAATTCGTGAAAGTTGATCAGCAAACCCTCTTCGACCTCATCCTGGTATGTTT------------------CTTGGTCTTGTTTTTTCTTGCTTGAGCATGATCTTTCGTTGCCTTTGTACATTCTTTTCAAATCTTTTGCTCAGCCGTTGTTGTTCCATGCTTTAAAGTCTGTAGATTCGGGAGTCTTTGCTGACTTTCCCCTT-CTATTGTTATGCACAGGCAGCAAATTACCTCAACATCATGAATCTGTTGGATCTGACCTGCCAGACCGTGGCAGACATGATCAAAGGCAAGACGCCAGAGGAGATTCGCAGTACTTTCAACATCAAGAACGATTTTACTCCAGAAGAAGAGGAA Osmunda_regalis_R13aR14a TCAGACTGTCGCCTTTGAATCCCAGACCATCAAGAACATGATCGAAGACACTGGCTGTGATGCCCCTATTCCCCTCCCTAACGTTTCCAGCAAGATCCTTGCCAAGGTCATTGAATTTTGTAAGTTCCATGTCAACTCTAAGAAGACTGGTGATGATGGTTGCGGTCCTTCCGAGGAGGAAGTTAAGTCCTTCGACGCTGAATTCGTGAAAGTTGATCAGCAAACCCTCTTCGACCTCATCCTGGTATGTTT------------------CTTGGTCTTGTTGTTTCTTGCTTGTGCATGATCTTTCGTTGCCTTTGTACATTCTTTTCAAATCTTTTGCTCAGCCGTTGTTGTTCCATGTTTTAAAGTTTGTAGATTCGGGAGTCTTTGCTGACTTTCCCCTT-CTATTGTTATGCACAGGCAGCAAATTACCTCAACATCATGAATCTGTTGGATCTGACCTGCCAGACCGTGGCAGACATGATCAAAGGCAAGACGCCAGAGGAGATTCGcAGTACTTTCAACATCAAgAACGATTTTACTCCAGAAGAAGAGGAA Osmunda_regalis_R14b TCAGACTGTCGCCTTTGAATCCCAGACCATCAAGAACATGATCGAAGACACTGGCTGTGATGCCCCTATTCCCCTCCCTAACGTTTCCAGCAAGATCCTTGCCAAGGTCATTGAATTTTGTAAGTTCCATGTCAACTCTAAGAAGACTGGTGATGATGGTTGCGGTCCTTCCGAGGAGGAAGTTAAGTCCTTCGACGCTGAATTCGTGAAAGTTGATCAGCAAACCCTCTTCGACCTCATCCTGGTATGTTT------------------CTTGGTCTTGTTGTTTCTTGCTTGTGCATGATCTTTCGTTGCCTTTGTACATTCTTTTCAAATCTTTTGCTCAGCCGTTGTTGTTCCATGTTTTAAAGTTTGTAGATTCGGGAGTCTTTGCTGACTTTCCCCTT-CTATTGTTATGCACAGGCAGCAAATTACCTCAACATCATGAATCTGTTGGATCTGACCTGCCAGACCGTGGCAGACATGATCAAAGGCAAGACGCCAGAGGAGATTCGtAGTACTTTCAACATCAAaAACGATTTTACTCCAGAAGAAGAGGAA Osmunda_regalis_R13bR17R18 TCAGACTGTCGCCTTTGAATCCCAGACCATCAAGAACATGATCGAAGACACTGGCTGTGATGCCCCTATTCCCCTCCCTAACGTTTCCAGCAAGATCCTTGCCAAGGTCATTGAATTTTGTAAGTTCCATGTCAACTCTAAGAAGACTGGTGACGATGGTTGCGGTCCTTCCGAGGAGGAAGTTAAGTCCTTCGACGCTGAATTCGTGAAAGTTGATCAGCAAACCCTCTTCGACCTCATCCTGGTATGTTT------------------CTTGGTCTTGTTGTTTCTTGCTTGTGCATGATCTTTCGTTGCCTTTGTACATTCTTTTCAAATCTTTTGCTCAGCCGTTGTTGTTCCATGTTTTAAAGTTTGTAGATTCGGGAGTCTTTGCTGACTTTCCCCTT-CTATTGTTATGCACAGGCAGCAAATTACCTCAACATCATGAATCTGTTGGATCTGACCTGCCAGACCGTGGCAGACATGATCAAAGGCAAGACGCCAGAGGAGATTCGTAGTACTTTCAACATCAAAAACGATTTTACTCCAGAAGAAGAGGAA Osmunda_lancea_L1L2L3 TCAGATTGTCGCCTTTGAATCCCAGACCATCAAGAACATGATCGAAGACACTGGCTGTGATGCCCCTATTCCCCTCCCTAACGTTTCCAGCAAGATCCTTGCCAAGGTCATTGAATTTTGTAAGTTCCATGTCAACTCTAAGAAGACTGGTGATGATGGTTGCGGTCCCTCCGAAGAGGAAGTCAAGTCCTTCGACGCTGAATTCGTGAAAGTTGATCAGCAAACCCTCTTCGACCTCATCCTGGTATGTTT------------------CTTGGTCTTCTTGTTTCTTGCTTGAGCATGATCTTTCGTTGCCTTTGTACATTCTTTTCAAATCTTTTGCTCAGCCGTTGTTGTTCCATGTTTTAAAGTTTGTAGATTCGGGAGTCTTTGCTGACTTTCCCCTT-CTATTGTTATGCACAGGCGGCAAATTACCTCAACATCATGAATCTTTTGGATCTGACCTGCCAGACCGTGGCAGACATGATCAAAGGCAAGACGCCAGAGGAGATTCGTAGTACTTTCAACATCAAGAACGATTTTACTCCAGAGGAAGAGGAA Osmunda_regalis_R5R6R7R8R9 TCAGATTGTCGCCTTTGAATCCCAGACCATCAAGAACATGATCGAAGACACTGGCTGTGATGCCCCTATTCCCCTCCCTAACGTTTCCAGCAAGATCCTTGCCAAGGTCATTGAATTTTGTAAGTTCCATGTCAACTCTAAGAAGACTGGTGATGATGGTTGCGGTCCCTCCGAGGAGGAAGTTAAGTCCTTCGACGCTGAATTCGTGAAAGTTGATCAGCAAACCCTCTTCGACCTCATCCTGGTATGTTT------------------CTTGGTCTTCTTGTTTCTTGCTTGAGCATGATCTTTCGTTGCCTTTGTACATTCTTTTCAAATCTTTTGCTCAGCCGTTGTTGTTCCATGCGTTAAAGTCTGTAGATTCGGGAGTCTTTGCTGACTTTCCCCTT-CTATTGTTATGCACAGGCAGCAAATTACCTCAACATCATGAATCTGTTGGATCTGACCTGCCAGACCGTGGCAGACATGATCAAAGGCAAGACGCCAGAGGAGATTCGCAGTACTTTCAACATCAAGAACGATTTTACTCCAGAAGAAGAGGAA Osmunda_regalis_R1R2R3R4 TCAGATTGTCGCCTTTGAATCCCAGACCATCAAGAACATGATCGAAGACACTGGCTGTGATGCCCCTATTCCCCTCCCTAACGTTTCCAGCAAGATCCTTGCCAAGGTCATTGAATTTTGTAAGTTCCATGTCAACTCTAAGAAGTCTGGTGATGATGGTTGCGGTCCCTCCGAGGAGGAAGTTAAGTCCTTCGACGCTGAATTCGTGAAAGTTGATCAGCAAACCCTCTTCGACCTCATCCTGGTATGTTT------------------CTTGGTCTTCTTGTTTCTTGCTTGAGCATGATCTTTCGTTGCCTTTGTACATTCTTTTCAAATCTTTTGCTCAGCCGTTGTTGTTCCATGCGTTAAAGTCTGTAGATTCGGGAGTCTTTGCTGACTTTCCCCTT-CTATTGTTATGCACAGGCAGCAAATTACCTCAACATCATGAATCTGTTGGATCTGACCTGCCAGACCGTGGCAGACATGATCAAAGGCAAGACGCCAGAGGAGATTCGCAGTACTTTCAACATCAAGAACGATTTTACTCCAGAAGAAGAGGAA Osmunda_regalis_R111R12 TCAAATTGTCGCCTTTGAATCCCAGACCATCAAGAACATGATCGAAGACACTGGCTGTGATGCCCCTATTCCCCTCCCTAACGTTTCCAGCAAGATCCTTGCCAAGGTCATTGAATTTTGTAAGTTCCATGTCAACTCTAAGAAGACTGGTGATGATGGTTGCGGTCCCTCCGAGGAGGAAGTTAAGTCCTTCGACGCTGAATTCGTGAAAGTTGATCAGCAAACCCTCTTCGACCTCATCCTGGTATGTTT------------------CTTGGTCTTCTTGTTTCTTGCTTGAGCATGACCTTTCGTTGCCTTTGTACATTCTTTTCAAATCTTTTGCTCAGCCGTTGTTGTTCCATGCGTTAAAGTCTGTAGATTCGGGAGTCTTTGCTGACTTTCCCCTT-CTATTGTTATGCACAGGCAGCAAATTACCTCAACATCATGAATCTGTTGGATCTGACCTGCCAGACCGTGGCAGACATGATCAAAGGCAAGACGCCAGAGGAGATTCGCAGTACTTTCAACATCAAGAACGATTTTACTCCAGAAGAAGAGGAA Osmunda_regalis_R16 TCAGACTGTCGCCTTTGAATCCCAGACCATCAAGAACATGATCGAAGACACTGGCTGTGATGCCCCTATTCCCCTCCCTAACGTTTCCAGCAAGATCCTTGCCAAGGTCATTGAATTTTGTAAGTTCCATGTCAACTCTAAGAAGACTGGTGATGATGGTTGCGGTCCCTCCGAGGAGGAAGTTAAGTCCTTCGACGCTGAATTCGTGAAAGTTGATCAGCAAACCCTCTTCGACCTCATCCTGGTATGTTT------------------CTTGGTCTTCTTGTTTCTTGCTTGAGCATGATCTTTCGTTGCCTTTGTAGATTCTTTTCAAATCTTTTGCTCAGCCGTTGTCGTTCCATGTTTTAAAGTCTGTAGATTCGGGAGTCTTTGCTGACTTTCCCCTT-CTATTGTTATGCACAGGCGGCAAATTACCTCAACATCATGAATCTTTTGGATCTGACCTGCCAGACCGTGGCAGACATGATCAAAGGCAAGACGCCAGAGGAGATTCGTAGTACTTTCAACATCAAGAACGATTTTACTCCAGAAGAAGAGGAA Claytosmunda_claytoniana_CL2 CCAGACTGTCGCCTTTGAATCCCAGACCATCAAGAACATGATTGAAGACACTGGCTGTGATGCCCCCATTCCCCTCCCTAATGTTTCCAGCAAGATCCTTGCAAAGGTCATTGAATTTTGTAAGTTCCATGTCAACTCTAAGAAGACTGGTGATGATGGTTGCGGTCCCTCCGAGGATGAAGTCAAGTCCTTCGACGCTGAATTCGTGAAAGTTGATCAGCAAACCCTCTTCGACCTCATCCTGGTATGCTTGGTTGGGTACTTGCTAAGCTTTTTGGTCTTGTTTCTTGCTTGAGCATGATCTTTCGTTGCCTCTGTACATTC-GTTCAAATCTTTTGCTCAGCCGTTGTTGTTCCATGTTTTAAAGTTTGTACATTCGGGAGTCTTTGCTGACCTTTCCCTTCCTATTGTTATGCACAGGCGGCAAATTACCTCAACATCATGAATCTGTTGGATCTGACCTGCCAGACCGTGGCAGACATGATCAAAGGCAAGACGCCAGAGGAGATTCGTAATACTTTCAACATCAAGAACGATTTTACTCCAGAAGAAGAGGAA ; END; BEGIN MRBAYES; Prset statefreqpr = dirichlet ( 1 , 1 , 1 , 1 ); Lset nst = 6 rates = propinv; log start filename = L418.log replace; mcmcp ngen = 10000000 printfreq = 1000 samplefreq = 100 nchains = 4 savebrlens = yes filename = L418Bayes; mcmc; log stop; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1- 559; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1- 559; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1- 559; END; BEGIN TREES; Title L418tree; ID 0174bf5391e827; LINK Taxa = Taxa; TRANSLATE [0] 1 Osmunda_regalis_R10, [1] 2 Osmunda_japonica_J1J2J3J4J5J6J7J8, [2] 3 Osmunda_regalis_R15, [3] 4 Osmunda_regalis_R13aR14a, [4] 5 Osmunda_regalis_R14b, [5] 6 Osmunda_regalis_R13bR17R18, [6] 7 Osmunda_lancea_L1L2L3, [7] 8 Osmunda_regalis_R5R6R7R8R9, [8] 9 Osmunda_regalis_R1R2R3R4, [9] 10 Osmunda_regalis_R111R12, [10] 11 Osmunda_regalis_R16, [11] 12 Claytosmunda_claytoniana_CL2; TREE con_50_majrule = (12:0.0259805,(11:0.00818,(2:0.002155,7:0.004306)0.98:0.008464,((1:0.006556,8:0.002157,9:0.004376,10:0.006534):0.007798,(3:0.009861,(4:0.002477,(5:0.002232,6:0.0043)0.99:0.006354)1.00:0.010326)0.58:0.005193)0.97:0.009273)0.96:0.0259805)[% ] [% ] [% setBetweenBits = selected ]; TREE con_50_majrule = (1:0.006556,8:0.002157,9:0.004376,10:0.006534,(((2:0.002155,7:0.004306):0.008464,11:0.00818,12:0.051961):0.009273,(3:0.009861,(4:0.002477,(5:0.002232,6:0.0043):0.006354):0.010326):0.005193):0.007798); END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1600937937923; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 2576656024912125526; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 7213052506819505417; mqVersion 361; checksumv 0 3 3813516246 null getNumChars 559 numChars 559 getNumTaxa 12 numTaxa 12 short true bits 1152921504606846991 states 15 sumSquaresStatesOnly 158235.0 sumSquares -2.30584300921354547E18 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState true false 296; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1155 923; setLocation 1270 177; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #7213052506819505417 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -72; setLocation 1270 177; 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; toggleReduceCellBorders off; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleShowPaleGrid off; toggleShowPaleCellColors off; toggleShowPaleExcluded off; togglePaleInapplicable on; togglePaleMissing off; toggleShowBoldCellText off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; getWindow; tell It; forceAutosize; endTell; hideWindow; 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;