#NEXUS
[written Wed Feb 25 12:30:27 PST 2026 by Mesquite  version 3.81 (build 955) at C02DH0Y9PN78/134.10.99.113]

BEGIN TAXA;
	TITLE Taxa;
	DIMENSIONS NTAX=10;
	TAXLABELS
		Aethionema_grandiflorum_DQ249867 Brassica_carinata_DQ003698 Brassica_juncea_GQ268062 Brassica_napus_DQ003666 Brassica_nigra_DQ003644 Brassica_oleracea_DQ003652 Brassica_rapa_DQ340642 Raphanus_raphanistrum_GQ268068 Raphanus_sativus_GQ268079 Sinapis_alba_AY722486 
	;

END;


BEGIN CHARACTERS;
	TITLE  Character_Matrix;
	DIMENSIONS  NCHAR=583;
	FORMAT DATATYPE = DNA GAP = - MISSING = ?;
	MATRIX
	Aethionema_grandiflorum_DQ249867  ACTCTCGGT-GAACCAG---GCTTTAACCGGTCCTGTGTTCACTGA-CTCCAAGTATCCGCGAA-CGTCCTT---CTCAGAGT----TCTCTTTGGGTTGGATTGTGACCG--GCTTTCCTTGGATATCACAAAACCCCGGCATTAAAAGTGCCAAGGAACATTGAAC-GAAATGGT--CTGCGTTTG-CGACCCGGAGACGGTGTATG--CAAACGTGGTGCCAGTATCTAAAGTCTA-AACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTCAAGCCTTCGGGCCGAGGGCACGTCTGCCTGGGTGTCACAAAACGTCGTCCCCC--CATCCA-TCTTGGATATGGGACGGAAGTTGGTCTCCCGTGTGGTACCGCACGCGGTTGGCCTAAATCCGAGCCAAGGGCA-GCAAGACTGTCCCGACTAGCGGTGGTGAACAAAAGC--CTCTTGTTATAGTCGGGTTGCTCTTCTTGTCCGTGAGCTTTAAGATG
	Brassica_carinata_DQ003698        ACTCTCGGT-GGGCCGG--TCTCTTAGCCGATTCCGTGCCTGCCGATTTCCGTGGTTATGTGTTCCGTCCCCGGTTCAAGACTTACTTAGGTCTCGGTCGGATCGTGCGCATAGCTTCC---GGATTTCACCAAACCCCGGCACGAAAAGTGTCAAGGAACATGCAAC-TAAACAGT--CTGCTTTCGCCAACCCGGAGACGGTGTTTGTTCGGAAGTAGTGCTGCAATGTAAAGTCTAAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCCAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACAAATCGTCGTCCCCC--CATCCTCTCGAGGATATGGGACGGAAGCTGGTCTCCCGTGTGTTACCGCACGCGGTTGGCCAAAATCCGAGCTAAGGGCG-CCAGGAGCGTCTCGACATGCGGTGGTGAATTCAAGC--CTCGTAATATCGTCG----GTCGTTCCGGTCCAAAAGCTCT-CGATG
	Brassica_juncea_GQ268062          ACTCTCGGT-AGGCCGG--TTTCTTA-------CTGTGCCTGCTGA-TTCCGTGGTTATGCGTT-CATCCTTGG-CCAAGACT----TCAGTTTTGGTTGGATCGTACGCATAGCTTCC---GGATATCACCAAACCCCGGCACGAAAAGTGTCAAGGAAAATGCAAC-TAAACAGC--CTGCTTTCGCCAACCCGGAGACGGTGTTTGTTCGGAAGCAGTGCTGCAATGTAAAGTCTAAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCCAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACAAATCGTCGTCCCCC--CATCCTCTCGAGGATATGGGACGGAAGCTGATCTCCCGTGTGTTACCGCACGCGGTTGGCCAAAATCCGAGCTAAGGACG-TCAGGAGCGTCTTGACATGCGGTGGTGAATTTAATT--CTCGTCATATAGTCA----GACGTTCCGGTCCAAAAGCTCT-TGATG
	Brassica_napus_DQ003666           ACTCTCGGT-AGGCCGG--TTTCTTA-------CTGTGCCTGCTGA-TTCCGTGGTTATGCGTT-CATCCTTGG-CCAAGACT----TCAGTTTTGGTTGGATCGTACGCATAGCTTCC---GGATATCACCAAACCCCGGCACGAAAAGTGTCAAGGAAAATGCAAC-TAAACAGC--CTGCTTTCGCCAACCCGGAGACGGTGTTTGTTCGGAAGCAGTGCTGCAATGTAAAGTCTAAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCCAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACAAATCGTCGTCCCCC--CATCCTCTCGAGGATATCGGACGGAAGCTGGTCTCCCGTGTGTTACCGCACGCGGTTGGCCAAAATCCTAGCTAAGGATG-CCAGGAGCGTCTTGACATGCGGTGGTGAATTCAATT--CTCGTCAAATCGTCA----GTCGTTTCGGTCCGAAAGCTCT-TGATG
	Brassica_nigra_DQ003644           ACTCTCGGT-GGGCCGG--TCTCTTAGCCGATTCCGTGCCTGCCGATTTCCGTGGTTATGTGTTCCGTCCCCGGTTCAAGACTTACTTAGGTCTCGGTCGGATCGTGCGCATAGCTTCC---GGATTTCACCAAACCCCGGCACGAAAAGTGTCAAGGAACATGCAAC-TAAACAGT--CTGCTTTCGCCAACCCGGAGACGGTGTTTGTTCGGAAGTAGTGCTGCAATGTAAAGTCTAAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCCAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACAAATCGTCGTCCCCC--CATCCTCTCGAGGATATGGGACGGAAGCTGGTCTCCCGTGTGTTACCGCACGCGGTTGGCCAAAATCCGAGCTAAGGGCG-CCAGGAGCGTCTCGACATGCGGTGGTGAATTCAAGC--CTCGTAATATCGTCG----GTCGTTCCGGTCCAGAAGCTCT-CGATG
	Brassica_oleracea_DQ003652        ACTCTCGGT-GGGCCGG--TTTCTTAGCTGATTTCGTGCCTACCGA-TTCCGTGGTTATGCGTT-CGTCACCGG-CC-----------CAGTTTCGGTTGGATCATACGCATAGCTTCC---GGATATCACCAAACCCCGGCACGAAAAGTGTCAAGGAACATTCAAC-TAAACGGC--CTGCTTTCGCCAACCCGGAGACGGTGTTTGTTCGGAAGCAGTGCTGCAATGTAAAGTCTAAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCCAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACAAATCGTCGTCCCCC--CATCCTCTCGAGGATATCGGACGGAAGCTGGTCTCCCGTGTGTTACCGCACGCGGTTGGCCAAAATCCTAGCTAAGGATG-CCAGGAGCGTCTTGACATGCGGTGGTGAATTCAATT--CTCGTCAAATCGTCA----GTCGTTTCGGTCCGAAAGCTCT-TGATG
	Brassica_rapa_DQ340642            ACTCTCGGT-AGGCCGG--TTTCTTA-------CTGTGCCTGCTGA-TTCCGTGGTTATGCGTT-CATCCTTGG-CCAAGACT----TCAGTTTTGGTTGGATCGTACGCATAGCTTCC---GGATATCACCAAACCCCGGCACGAAAAGTGTCAAGGAAAATGCAAC-TAAACAGC--CTGCTTTCGCCAACCCGGAGACGGTGTTTGTTCGGAAGCAGTGCTGCAATGTAAAGTCTAAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCCAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACAAATCGTCGTCCCCC--CATCCTCTCGAGGATATGGGACGGAAGCTGATCTCCCGTGTGTTACCGCACGCGGTTGGCCAAAATCCGAGCTAAGGACG-TCAGGAGCGTCTTGACATGCGGTGGTGAATTTAATT--CTCGTCATATAGTCA----GACGTTCCGGTCCAAAAGCTCT-TGATG
	Raphanus_raphanistrum_GQ268068    ACTCTCGGC-GGGACGG--TTTCTTAGCCGATCCTGTTCCCGCCGA-TTCCAAGGCTCTGCGTATGGTCCT------------------AATCCCGGTTAGATCATGCGCTTAGTTTCT---GGAAATCACAAAACCCCGGCACGAAAAGTGTCAAGGAACATGCAACAAAAACAGC--CTGCGTTCGCCTACCCGGAGACGGTGTGTGCGCGGACGCTGTGCTGCAATATAAAGTCTAAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCCAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACAAATCGTCGTCCCCC--CATCCT-TTGAGGATACGGGACGGAAGCTGGTCTCCCGTGTGTTACCGCACGCGGTTGGCCAAAATCCGAGCTAAGGACG-CAAGGAGCGTCCCGACATGCGGTGGTGAATTCAAGC--CTCGTCATATCGTCG----GTCGCTCCTGTCCGGAAACTCT-AGATG
	Raphanus_sativus_GQ268079         ACTCTCGGT-GGGCTGGGTTCTCTTACCGGAATCCATGCCTTCCGA-TTCCGTGGTTATGTGTTTCGTCCCCGG-TCAAGGCT----------------GGGTCGTGCACATAGCTTCC---GGAGATCACCAAACCCCGGCACGAAAAGTGTCAAGGAACATGCAAC-TAAACAGT--CTGCTTTCGCCAACCCGGAAACGGTGTTTGTTCGGAAACAGTTCTGAAATGTAAAGTCTATAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCCAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACAAATCGTCGTCCCCC--CATCCTCTCGAGGATATAGGACGGAAGCTGGTCTCCCGTGTGTTACCGCACGCGGTTGGCCAAAATCCGAGCTAAGGATG-CCAGGAGCGTCTTGACATGCGGTGGTGAATTCAATCTCCTCGTCATATCGTCG----GTCGTTCCGGTCCAAAAGCTCT-CGATG
	Sinapis_alba_AY722486             ACTCTCGGT-GGGCCGG--TTTCTTTGCTGATTCTGTGCCTGCCGA-TTCCGTGGTTATGCGTTAAGTTCCCAG-CCAGTACT----TCGGTCTTGGTTGGGTCTTGCGCATTGCTTCC---GGATATCACCAAACCCCGGCACGAAAAGTGTCAAGGAACATTCAAC-TAGGTAGC--CTGCGTTCGCCAACCCGGAGACGGTGTTTGTGCGGAAGCTGTGCTGCAATGTAAAGTCTAAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCCAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACAAATCGTCGTCCCCC--CATCCTCTCGAGGATATGGGACGGAAGCTGGTCTCCCGTGTGTTACCGCACGCGGTTGGCCAAAATCCGAGCTAAGGACGTTTTGGAGCGTCTCGACATGCGGTGGTGAATTGTAAC--CTCGTCATATTGTCG----GTCGTTCCGGTTCAAAAGCTCT-TGATG

;



END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  unord:  1- 583;

END;

BEGIN NOTES;

	TAXABITS   NAME = newlyAddedTaxon on =  1 -  10;

END;

BEGIN CODONS;
	CODESET * UNTITLED   =  universal:  1- 583;


END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  'Jukes-Cantor':  1- 583;
END;

Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		timeSaved 1772051427041;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 8994094395027138411;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 5970969199257487754;
			mqVersion 381;
			checksumv 0 3 2462167454 null  getNumChars 583 numChars 583 getNumTaxa 10 numTaxa 10   short true   bits 15   states 15   sumSquaresStatesOnly 116954.0 sumSquares 116954.0 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 1901 943;
			setLocation 37 25;
			setFont SanSerif;
			setFontSize 10;
			getToolPalette;
			tell It;
			endTell;
			desuppress;
		endTell;
		getEmployee  #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
		tell It;
			showDataWindow #5970969199257487754 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					getTable;
					tell It;
						rowNamesWidth 325;
					endTell;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 1801 871;
					setLocation 37 25;
					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;
					toggleReduceCellBorders off;
					toggleAutoWCharNames off;
					toggleAutoTaxonNames off;
					toggleShowDefaultCharNames off;
					toggleConstrainCW on;
					toggleBirdsEye off;
					toggleColorOnlyTaxonNames off;
					toggleShowPaleGrid off;
					toggleShowPaleCellColors off;
					toggleShowPaleExcluded off;
					togglePaleInapplicable on;
					togglePaleMissing off;
					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 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.chromaseq.ColorQuality.ColorQuality;
				tell It;
					toggleAmbiguities on;
					toggleMarks on;
				endTell;
				getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor;
				tell It;
					panelOpen false;
				endTell;
				getEmployee #mesquite.chromaseq.SourceFileInfoEditor.SourceFileInfoEditor;
				tell It;
					panelOpen false;
				endTell;
			endTell;
		endTell;
		endTell;
end;