#NEXUS
[written Thu Sep 24 17:01:16 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_J6J7J8 Osmunda_japonica_J12J3J4J5 Osmunda_regalis_R13R14R15R16R17R18 Osmunda_lancea_L1bL2 Osmunda_lancea_L1aL3 Osmunda_regalis_R5R6R7R8R9 Osmunda_regalis_R1R3 Osmunda_regalis_R2R4 Osmunda_regalis_R11R12 Plenasium_banksiifolium Claytosmunda_claytoniana_CL1CL2 
	;

END;


BEGIN CHARACTERS;
	TITLE  Character_Matrix;
	DIMENSIONS  NCHAR=198;
	FORMAT DATATYPE = DNA GAP = - MISSING = ?;
	MATRIX
	Osmunda_regalis_R10                 TCACAAAGGTTGATCTTAGCACCACTGTTTTGGGATTCAAGATTTCCATGCCTATCATGGTTGCACCTACAGCAATGCAAAGAATGGCCCACCCAGAAGGTACGCTTGATGATAATATGGTTATTGTATTGGCTCGTTCTTGGTTTTT-TCTAAATAGATTGATGATATCAGTTTATAACATGCTTGCCAATATTAAA
	Osmunda_japonica_J6J7J8             TCACAAAGGTTGATGTAAGCACCACTGTTTTGGGATTCAAGATTTCCATGCCTATCATGGTTGCACCTACAGCATTTCAAAGAATGGCCCACCCAGAAGGTACGCTTAATGATAATATGGTTATTGTATTGGCTCGTTCTTCGTTTTTGTCTAAATAGATTGATGATATCAGTTTATAACATGCTTGCCAATATTAAA
	Osmunda_japonica_J12J3J4J5          TCACAAAGGTCGATGTAAGCACCACTGTTTTGGGATTCAAGATTTCCATGCCTATCATGGTTGCACCTACAGCATTTCAAAGAATGGCCCACCCAGAAGGTACGCTTGATGATAATATGGTTATTGTATTGGCTCGTTCTTCGTTTTTGTCTAAATAGATTGATGATATCAGTTTATAACATGCTTGCCAATATTAAA
	Osmunda_regalis_R13R14R15R16R17R18  TCACAAAGGTTGATCTAAGCACAACTGTTTTGGGATTCAAGATTTCCATGCCTATCATGGTTGCACCTACGGCATTTCAGAGAATGGCCCACCCAGAAGGTACGCTTGATGATAATATGGTTATTGTATTGGCTCGTTCTTCATTTTT-TCTAAATAGATTGATGATATCAGTTTATAACATGCTTGCCAATATTAAA
	Osmunda_lancea_L1bL2                TCACAAAGGTTGATGTAAGCACCACTGTTTTGGGATTCAAGATTTCCATGCCTATCATGGTTGCACCTACAGCATTTCAAAGAATGGCCCACCCAGAAGGTACGCTTGATGATAATATGGTTATTGTATTGGCTCGTTCTTCGTTTTTGTCTAAATAGATTGATGAAATCAGTTTATAACATGCTTGCCAATATTAAA
	Osmunda_lancea_L1aL3                TCACAAAGGTTGATGTAAGCACCACTGTTTTGGGATTCAAGATTTCCATGCCTATCATGGTTGCACCTACAGCATTTCAAAGAATGGCCCACCCAGAAGGTACGCTTGATGATAATATGGTTATTGTATTGGCTCGTTCTTCGTTTTTGTCTGAATAGATTGATGAAATCAGTTTATAACATGCTTGCCAATATTAAA
	Osmunda_regalis_R5R6R7R8R9          TCACAAAGGTTGATCTAAGCACCACTGTTTTGGGATTCAAGATTTCCATGCCCATCATGGTTGCACCTACAGCAATGCAAAGAATGGCCCACCCAGAAGGTACGCTTGATGATAATATGGTTATTGTATTGGCTCGTTCTTCGTTTTT-TCTAAATAGATTGATGATATCAGTTTATAACATGCTTGCCAATATTAAA
	Osmunda_regalis_R1R3                TCACAAAGGTTGATTTAAGCACCACTGTTTTGGGATTCAAGATTTCCATGCCTATCATGGTTGCACCTACAGCAATGCAAAGAATGGCCCACCCAGAAGGTACGCTTGATGATAATATGGTTATTGTATTGGCTCGTTCTTCGTTTTT-TCTAAATAGATTTATGATATCAGTTTATAACATGCTTGCCAATATTAAA
	Osmunda_regalis_R2R4                TCACAAAGGTTGATCTAAGCACCACTGTTTTGGGATTCAAGATTTCCATGCCTATCATGGTTGCACCTACAGCAATGCAAAGAATGGCCCACCCAGAAGGTACGCTTGATGATAATATGGTTATTGTATTGGCTCGTTCTTCGTTTTT-TCTAAATAGATTTATGATATCAGTTTATAACATGCTTGCCAATATTAAA
	Osmunda_regalis_R11R12              TCACAAAGGTTGATCTAAGCACCACTGTTTTGGGATTCAAGATTTCCATGCCTATCATGGTTGCACCTACAGCAATGCAAAGAATGGCCCACCCAGAAGGTACGCTTGATGATAATATGGTTATTGTATTGGCTCGTTCTTGGTTTTT-TCTAAATAGATTGATGATATCAGTTTATAACATGCTTGCCAATATTAAC
	Plenasium_banksiifolium             TCTCAAAGGTTGATCTAAGCACAACTGTTTTGGGATTCAAGATTTCCATGCCTATCATGGTTGCACCTACAGCAATGCAAAGAATGGCCCACCCAGAAGGTACGCTTGATGATAATATGGTTATTGTAT-GGCTGGTTGTTCGTTTTT--CTAAATAGATTGACGATATCAGTTCATAACATATTTTCCAATATTAAA
	Claytosmunda_claytoniana_CL1CL2     TCACAAAGGTTGATCTAAGCACAACTGTTTTGGGATTCAAGATTTCCATGCCTATCATGGTTGCACCTACAGCAATGCAAAGAATGGCCCACCCTGAAGGTACGCTTGATGAGAATATGGTTATTGTATTGGCTCGTTCTTCGCTTTT-TCTACATAGATTGATGATATTAGTTTGTAACATGTTTGCCAATATTAAA

;



END;

BEGIN MRBAYES;
	Prset statefreqpr = dirichlet ( 1 , 1 , 1 , 1 );
	Lset nst = 2 rates = equal;
log start filename = L58.log replace;
mcmcp ngen = 10000000 printfreq = 1000 samplefreq = 100
 nchains = 4 savebrlens = yes filename = L58Bayes;
mcmc;
log stop;

END;
BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  unord:  1- 198;

END;

BEGIN CODONS;
	CODESET * UNTITLED   =  universal:  1- 198;


END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  'Jukes-Cantor':  1- 198;
END;

BEGIN TREES;
	Title L58tree;
	ID 0174bf1e49789;
	LINK Taxa = Taxa;
	TRANSLATE
[0] 		1 Osmunda_regalis_R10,
[1] 		2 Osmunda_japonica_J6J7J8,
[2] 		3 Osmunda_japonica_J12J3J4J5,
[3] 		4 Osmunda_regalis_R13R14R15R16R17R18,
[4] 		5 Osmunda_lancea_L1bL2,
[5] 		6 Osmunda_lancea_L1aL3,
[6] 		7 Osmunda_regalis_R5R6R7R8R9,
[7] 		8 Osmunda_regalis_R1R3,
[8] 		9 Osmunda_regalis_R2R4,
[9] 		10 Osmunda_regalis_R11R12,
[10] 		11 Plenasium_banksiifolium,
[11] 		12 Claytosmunda_claytoniana_CL1CL2;
	TREE con_50_majrule = (12:0.017891,(11:0.041466,(7:0.00967,(1:0.009867,10:0.009836):0.009726,(8:0.009859,9:0.004997)0.97:0.009781,(4:0.024819,(2:0.009721,3:0.009715,(5:0.004931,6:0.00971)0.98:0.009702)0.94:0.010266)0.98:0.014994)0.97:0.014245)0.94:0.017891)[% ] [% ] [%  setBetweenBits = selected ];
	TREE con_50_majrule = (1:0.009867,10:0.009836,(((2:0.009721,3:0.009715,(5:0.004931,6:0.00971):0.009702):0.010266,4:0.024819):0.014994,7:0.00967,(8:0.009859,9:0.004997):0.009781,(11:0.041466,12:0.035782):0.014245):0.009726);

END;


Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		timeSaved 1600934476867;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 6660470229216534696;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 1509919880410760498;
			mqVersion 361;
			checksumv 0 3 4192824557 null  getNumChars 198 numChars 198 getNumTaxa 12 numTaxa 12   short true   bits 15   states 15   sumSquaresStatesOnly 60950.0 sumSquares 60950.0 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 1546 924;
			setLocation 370 219;
			setFont SanSerif;
			setFontSize 10;
			getToolPalette;
			tell It;
			endTell;
			setActive;
			desuppress;
		endTell;
		getEmployee  #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
		tell It;
			showDataWindow #1509919880410760498 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 0 -72;
					setLocation 370 219;
					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;