#NEXUS [written Thu Sep 24 17:31:10 JST 2020 by Mesquite version 3.61 (build 927) at tsutsumichie-no-iMac.local/202.220.64.189] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=14; TAXLABELS Osmunda_regalis_R10 Osmunda_japonica_J6J7J8 Osmunda_japonica_J2J3J4J5 Osmunda_lancea_L1L2 Osmunda_japonica_J1a Osmunda_japonica_J1b Osmunda_lancea_L3 Osmunda_regalis_R1R2R4 Osmunda_regalis_R3 Osmunda_regalis_R11R12 Osmunda_regalis_R5R6R7R13R14R15R16aR17R18 Osmunda_regalis_R16b O84_L261.seq Osmunda_regalis_R8R9 ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=322; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Osmunda_regalis_R10 GGTCTAGCAGCTGAGATAATTGGAACCTTCGTTCTCGTATACACCGTCTTCTCTGCTACAGACCCAAAGAGGAACGCCCGGGATTCTCACGTTCCAGTATGTTAATCTGCCCCTGCGAGCTGGTTTGAGTGGAGTGAGAAATTCTGCTCGGTCTTGCTGTGTAAAGAGCGAAGATGAGGGCAAGTAAGGTCGTGTTGCGAGAGAGAGAG--TGAGTGAGAGGAGATCACTGAGCTTGTTATGTTTGCGCAGGTACTAGCTCCACTCCCCATCGGCTTCGCAGTGTTCATGGTGCATTTAGCAACTATTCCAATCACGGGCAC Osmunda_japonica_J6J7J8 GGTCTAGCAGCTGAGATAATTGGAACCTTCGTTCTCGTATACACCGTCTTCTCTGCTACAGACCCAAAGAGGAACGCCCGGGATTCTCACGTTCCAGTATGTTAATCTGCCTCTGCGAGCTGGTTTGAGCGGAGTGAGAAATTCTGCTCGGTCTTGCTGTGTAAAGAGCAAAGATGAGGGCAAGTAAGGTCGTGTTGCGAGAGAGAGAG--TGAGTGAGAGGAGATGACTGAGCTTGTTATGTTTGCGCAGGTTCTAGCTCCACTCCCCATCGGCTTCGCAGTGTTCATGGTGCATTTAGCAACGATTCCAATCACGGGCAC Osmunda_japonica_J2J3J4J5 GGTCTAGCAGCTGAGATAATTGGAACCTTCGTTCTCGTATACACCGTCTTCTCTGCTACAGACCCAAAGAGGAACGCCCGGGATTCTCACGTTCCAGTATGTTAATCTGCCTCTGCGAGCTGGTTTGAGCGGAGTGAGAAATTTTGCTCGGTCTTGCTGTGTAAAGAGCAAAGATGAGGGCAAGTAAGGTCGTGTTGCGAGAGAGAGAG--TGAGTGAGAGGAGATGACTGAGCTTGTTATGTTTGCGCAGGTTCTAGCTCCACTCCCCATCGGCTTCGCAGTGTTCATGGTGCATCTAGCAACTATTCCAATCACGGGCAC Osmunda_lancea_L1L2 GGTCTAGCAGCTGAGATAATTGGGACCTTCGTTCTCGTATACACCGTCTTCTCTGCTACAGACCCAAAGAGGAACGCCCGGGATTCTCACGTTCCAGTATGTTAATCTGCCTCTGCGAGCTGGTTTGAGCGGAGTGAGAAATTCTGCTCGGTCTTGCTGTGTAAAGAGCAAAGATGAGGGCAAGTAAGGTCGTGTTGCGAGAGAGAGAG--TGAGTGAGAGGAGATGACTGAGCTTGTTGTGTTTGCGCAGGTTCTAGCTCCACTCCCCATCGGCTTCGCAGTGTTCATGGTGCATTTAGCAACTATTCCAATCACGGGCAC Osmunda_japonica_J1a GGTCTAGCAGCTGAGATAATTGGAACCTTCGTTCTCGTATACACCGTCTTCTCTGCTACAGACCCAAAGAGGAACGCCCGGGATTCTCACGTTCCAGTATGTTAATCTGCCTCTGCGAGCTGGTTTGAGCGGAGTGAGAAATTCTGCTCGGTCTTGCTGTGTAAAGAGCAAAGATGAGGGCAAGTAAGGTCGTGTTGCGAGAGAGAGAG--TGAGTGAGAGGAGATGACTGAGCTTGTTATGTTTGCGCAGGTTCTAGCTCCACTCCCCATCGGCTTCGCAGTGTTCATGGTGCATcTAGCAACTATTCCAATCACGGGCAC Osmunda_japonica_J1b GGTCTAGCAGCTGAGATAATTGGAACCTTCGTTCTCGTATACACCGTCTTCTCTGCTACAGACCCAAAGAGGAACGCCCGGGATTCTCACGTTCCAGTATGTTAATCTGCCTCTGCGAGCTGGTTTGAGCGGAGTGAGAAATTCTGCTCGGTCTTGCTGTGTAAAGAGCAAAGATGAGGGCAAGTAAGGTCGTGTTGCGAGAGAGAGAG--TGAGTGAGAGGAGATGACTGAGCTTGTTATGTTTGCGCAGGTTCTAGCTCCACTCCCCATCGGCTTCGCAGTGTTCATGGTGCATtTAGCAACTATTCCAATCACGGGCAC Osmunda_lancea_L3 GGTCTAGCAGCTGAGATAATTGGGACCTTCGTTCTCGTATACACCGTCTTCTCTGCTACAGACCCAAAGAGGAACGCCCGGGATTCTCACGTTCCAGTATGTTAATCTGCCTCTGCGAGCTGGTTTGAGCGGAGTGAGAAATTCTGCTCGGTCTTGCTGTGTAAAGAGCAAAGATGAGGGCAAGTAAGGTCGTGTTGCGAGAGAGAGAG--TGAGTGAGAGGAGATGACTGAGCTTGTTATGTTTGCGCAGGTTCTAGCTCCACTCCCCATCGGCTTCGCAGTGTTCATGGTGCATTTAGCAACTATTCCAATCACGGGCAC Osmunda_regalis_R1R2R4 GGTCTAGCAGCTGAGATAATTGGAACCTTCGTTCTCGTATACACCGTCTTCTCTGCTACAGACCCAAAGAGGAACGCTCGGGATTCTCACGTTCCAGTATGTTAATCTGCCCCTGCGAGCTGGTTTGAGTGGAGTGAGAAATTCTGCTCGGTCTTGCTGTGTAAAGAGCAAAGATGAGGGCAAGTAAGGTCGTGTTGCGAGAGAGAGAG--TGAGTGAGAGGAGATGACTGAGCTTGTTATGTTTGCGCAGGTTCTAGCTCCACTCCCCATCGGCTTCGCAGTGTTCATGGTGCATTTAGCAACTATTCCAATCACGGGCAC Osmunda_regalis_R3 GGTCTAGCAGCTGAGATAATTGGAACCTTCGTTCTCGTATACACCGTCTTCTCTGCTACAGACCCAAAGAGGAACGCTCGGGATTCTCACGTTCCAGTATGTTAATCTGCCCCTGCGAGCTGGTTTGAGTGGAGTGAGAAATTCTGCTCGGTCTTGCTGTGTAAAGAGCAAAGATGAGGACAAGTAAGGTCGTGTTGCGAGAGAGAGAG--TGAGTGAGAGGAGATGACTGAGCTTGTTATGTTTGCGCAGGTTCTAGCTCCACTCCCCATCGGCTTCGCAGTGTTCATGGTGCATTTAGCAACTATTCCAATCACGGGCAC Osmunda_regalis_R11R12 GGTCTAGCAGCTGAGATAATTGGAACCTTCGTTCTCGTATACACCGTCTTCTCTGCTACAGACCCAAAGAGGAACGCCCGGGATTCTCACGTTCCAGTATGTTAATCTGCCCCTGCGAGCTGGTTTGAGCGGAGTGAGAAATTCTGCTCGGTCTTGCTGTGTAAAGAGCAAAGATGAGGGCAAGTAAGGTCGTGTTGCGAGAGAGAGAG--TGAGTGAGAGGAGATCACTGAGCTTGTTATGTTTGCGCAGGTACTAGCGCCACTCCCCATCGGCTTCGCAGTGTTCATGGTGCATTTAGCAACTATTCCAATCACGGGCAC Osmunda_regalis_R5R6R7R13R14R15R16aR17R18 GGTCTAGCAGCTGAGATAATTGGAACCTTCGTTCTCGTATACACCGTCTTCTCTGCTACAGACCCAAAGAGGAACGCCCGGGATTCTCACGTTCCAGTATGTTAATCTGCCCCTGCGAGCTGGTTTGAGCGGAGTGAGAAATTCTGCTCGGTCTTGCTGTGTAAAGAGCAAAGATGAGGGCAAGTAAGGTCGTGTTGCGGGAGAGAGAG--TGAGTGAGAGGAGATGACTGAGCTTGTAATGTCTGCGCAGGTACTAGCTCCACTCCCCATCGGCTTCGCAGTGTTCATGGTGCATTTAGCAACTATTCCAATCACGGGCAC Osmunda_regalis_R16b GGTCTAGCAGCTGAGATAATTGGAACCTTCGTTCTCGTATACACCGTCTTCTCTGCTACAGACCCAAAGAGGAACGCCCGGGATTCTCACGTTCCAGTATGTTAATCTGCCCCTGCGAGCTGGTTTGAGCGGAGTGAGAAATTCTGCTCGGTCTTGCTGTGTAAAGgGCAAAGATGAGGGCAAGTAAGGTCGTGTTGCGGGAGAGAGAG--TGAGTGAGAGGAGATGACTGAGCTTGTAATGTCTGCGCAGGTACTAGCTCCACTCCCCATCGGCTTCGCAGTGTTCATGGTGCATTTAGCAACTATTCCAATCACGGGCAC O84_L261.seq GGTCTAGCAGCTGAGATAATTGGAACCTTCGTTCTCGTGTACACCGTCTTCTCTGCTACCGACCCCAAGAGGAACGCCCGGGATTCTCACGTTCCAGTATGTCAATCTGCCCCTGCAAGCTGGTTTGTGTGGAGTGAA--------CTCGGTGTTGCTGTGTAAAGAGCAAAGATGAGGCCTAGTGAGGTCGTGTTGAGAGAGAGAGAGA-T-AGAGAGAG-AGATGACTGAGCTTGTTATGTTTGTGCAGGTACTAGCTCCACTTCCCATCGGCTTCGCCGTGTTCATGGTGCATTTAGCAACTATTCCAATCACGGGCAC Osmunda_regalis_R8R9 GGTCTAGCAGCTGAGATAATTGGAACCTTCGTTCTCGTATACACCGTCTTCTCTGCTACAGACCCAAAGAGGAACGCTCGGGATTCTCACGTTCCAGTATGTTAATCTGCCCCTGCGAGCTGGTTTGAGTGGAGTGAGAAATTCTGCTCGGTCTTGCTGTGTAAAGAGCAAAGATGAGGGCAAGTAAGGTCGTGTTGCGAGAGAGAGAGAGTGAGTGAGAGGAGATGACTGAGCTTGTTATGTTTGCGCAGGTTCTAGCTCCACTCCCCATCGGCTTCGCAGTGTTCATGGTGCATTTAGCAACTATTCCAATCACGGGCAC ; END; BEGIN MRBAYES; Prset statefreqpr = fixed ( equal ); Lset nst = 2 rates = gamma; log start filename = L261.log replace; mcmcp ngen = 10000000 printfreq = 1000 samplefreq = 100 nchains = 4 savebrlens = yes filename = L261Bayes; mcmc; log stop; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1- 322; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1- 322; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1- 322; END; BEGIN TREES; Title L261tree; ID 0174bf3a964f23; LINK Taxa = Taxa; TRANSLATE [0] 1 Osmunda_regalis_R10, [1] 2 Osmunda_japonica_J6J7J8, [2] 3 Osmunda_japonica_J2J3J4J5, [3] 4 Osmunda_lancea_L1L2, [4] 5 Osmunda_japonica_J1a, [5] 6 Osmunda_japonica_J1b, [6] 7 Osmunda_lancea_L3, [7] 8 Osmunda_regalis_R1R2R4, [8] 9 Osmunda_regalis_R3, [9] 10 Osmunda_regalis_R11R12, [10] 11 Osmunda_regalis_R5R6R7R13R14R15R16aR17R18, [11] 12 Osmunda_regalis_R16b, [12] 13 O84_L261.seq, [13] 14 Osmunda_regalis_R8R9; TREE con_50_majrule = (13:0.0303775,((1:0.008759,10:0.007151):0.006287,(11:0.003167,12:0.006228)1.00:0.01308,((8:0.003094,9:0.006229,14:0.003112)0.97:0.008872,(2:0.006292,6:0.003164,(3:0.006357,5:0.003241)0.96:0.006227,(4:0.006347,7:0.003228)0.96:0.006248)0.94:0.007206)0.81:0.006491)0.83:0.0303775)[% ] [% ] [% setBetweenBits = selected ]; TREE con_50_majrule = (1:0.008759,10:0.007151,(((2:0.006292,(3:0.006357,5:0.003241):0.006227,(4:0.006347,7:0.003228):0.006248,6:0.003164):0.007206,(8:0.003094,9:0.006229,14:0.003112):0.008872):0.006491,(11:0.003167,12:0.006228):0.01308,13:0.060755):0.006287); END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1600936270220; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8867775337140639101; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 4608096085371262868; mqVersion 361; checksumv 0 3 4002440526 null getNumChars 322 numChars 322 getNumTaxa 14 numTaxa 14 short true bits 1152921504606846991 states 15 sumSquaresStatesOnly 100581.0 sumSquares -4.6116860184273336E18 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 1149 1213; setLocation 1215 76; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #4608096085371262868 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -72; setLocation 1215 76; 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;