#NEXUS
[written Fri Aug 22 15:25:18 CDT 2014 by Mesquite  version 2.75 (build 564) at rachel-coburns-macbook-pro.local/10.0.1.17]

BEGIN TAXA;
	TITLE Taxa;
	DIMENSIONS NTAX=7;
	TAXLABELS
		Petunia_hybrida_AF022142 Nicotiana_benthamiana_V0.4.2Scf2714_ Solanum_lycopersicum_HQ008775 Solanum_tuberosum_AY102035 Iochroma_cyaneum_KJ094352 Iochroma_calycinum_KJ094347 Iochroma_calycinum_KJ094358 
	;

END;


BEGIN CHARACTERS;
	TITLE  F3H_Alignment;
	DIMENSIONS  NCHAR=1113;
	FORMAT DATATYPE = DNA GAP = - MISSING = ?;
	MATRIX
	Petunia_hybrida_AF022142              ATGGCACCTTCAACATTAACAGCATTAGCAGAAGAAAAGACCCTTCAAACAAGTTTCATTAGGGATGAAGATGAACGTCCAAAAGTGGCTTACAACCAATTCAGCAATGAGATCCCAATTATCTCGTTAGAGGGCATTGATGATGAA------------ACTGGTAAAAGAGCTGAAATATGTGACAAGATTGTTAAGGCATGTGAAGATTGGGGCGTTTTTCAAGTTGTGGATCATGGGGTTGATGCTGAACTTATTTCCCAAATGACAACTTTTGCTAAAGAATTCTTTGCTTTGCCTCCTGAGGAAAAGCTGCGGTTTGACATGTCTGGTGGCAAGAAAGGTGGATTTATTGTCTCTAGCCATCTACAGGGTGAAGTGGTCCAAGATTGGCGTGAAATTGTGACCTACTTTTCGTACCCAACAAGGGCAAGAGACTACTCTAGATGGCCAGACAAACCAGAAGGATGGATAGCTGTGACTCAGAAATATAGTGAAAAGTTAATGGAGTTAGCTTGCAAGTTATTGGATGTCCTATCAGAGGCTATGGGCTTGGAGAAGGAGGCCTTAACCAAGGCATGTGTGGATATGGACCAAAAAGTGGTTGTCAATTTTTACCCAAAGTGTCCTGAGCCTGACCTTACCCTTGGACTGAAAAGACACACTGATCCAGGAACCATCACTCTCTTGTTACAAGACCAAGTTGGTGGGCTTCAAGCTACTAAAGATAATGGCAAAACTTGGATCACTGTTCAGCCTGTTGAAGGTGCTTTTGTTGTCAATCTTGGTGACCACGGTCATTTTTTGAGCAATGGACGGTTCAAGAATGCTGATCATCAAGCAGTGGTGAACTCAAATAGCAGCAGGTTATCGATAGCCACGTTTCAGAATCCGGCACCAGAGGCGATAGTGTATCCATTGAAAATTAGGGAAGGAGAGAAGTCAATAATGGATGAGCCCATAACATTTGCAGAAATGTACAGAAGGAAAATGAGCAAGGATTTAGAACTTGCTAGGCTCAAGAAGCAGGCCAAGGAGCAGCAGTTACAAGCTGAAGTTGCTGCTGAGAAGGCTAAGTTGGAGTCCAAGCCCATTGAGGAAATTCTTGCTTAA
	Nicotiana_benthamiana_V0.4.2Scf2714_  ATGGCACCTTCGACATTAACAGCTCTAGCAGAGGAAAAGACACTTGAAACAAGTTTCATAAGAGATGAAGATGAGCGTCCAAAAGTGGCATACAACCAATTCAGCAACGAGATTCCGGTCATATCGTTGAAGGGTATTGATGATGAGAGTGGAGTTAATAGTGAAAGAAGAGGTGATATATGTGAAAAGATTGTCAAGGCATGTGAAGATTGGGGCATTTTCCAGGTAGTTGATCATGGTGTTGATGCTCAACTTATCTCACAAATGACAACTCTCGCTAAACAATTCTTCGCTTTGCCTCCTGAGGAAAAGTTACGCTTTGACATGTCTGGTGGCAAGAAAGGTGGCTTTATAGTCTCTAGCCATTTACAGGGTGAAGTGGTCCAAGATTGGCGTGAAATAGTGACCTATTTCTCATACCCAATTCGGGCTAGAGACTACTCTAGATGGCCAGACAAACCAGAGGGATGGATGGATGTGACTCAGAAGTACAGTGAAAAGTTAATGGAGTTGGCTTGCAAATTATTGGAAGTACTATCAGAGGCTATGGGCTTAGAGAATGATGCCTTAACCAAGGCCTGTGTGGATATGGACCAAAAAGTGGTTGTCAATTTTTACCCAAAGTGTCCACAGCCCGACCTTACCCTTGGGCTGAAACGACACACTGATCCAGGAACCATTACCCTCTTGTTACAAGACCAAGTTGGTGGGCTTCAAGCCACTAAAGATAAGGGCAAAACTTGGATTACTGTTCAGCCCGTTGAAGGCGCTTTTGTTGTCAATCTTGGGGACCATGGTCAGTTTTTGAGCAATGGAAGGTTTAAGAACGCTGATCATCAAGCAGTGGTGAACTCGAATAGCAGCAGATTATCGATAGCTACGTTTCAGAATCCAGCACCGGAGGCTATTGTGTACCCATTGAAAATTAGGGAAGGAGAGAAGGCAGTAATGAACGAGGCCATAACATTTGCAGAAATGTACAGGAGGAAAATGAGTAAGGACCTTGAGCTTGCTAGGCTCAAGAAACTGGCCAAGGAGCAGCAAATACAAGCTGAAGAAGCCACTGAGAAGGCCAAGTTGGAAACTAAGCCCATTGAAGAAATTCTTGCTTAA
	Solanum_lycopersicum_HQ008775         ATGGCACCTTCAACACTAACAGCTTTAGCTAATGAAAAGACCCTTGAAACAAGTTTTATTAGGGATGAAGAAGAACGTCCAAAAGTTGCTTACAATAAATTTAGTGACGAAATTCCAGTAATATCGTTGCAAGGTATTGATGAT---------GTTAAT---GGAAGAAGAAGTGAAATATGTGAGAGAATCGTAAATGCTTGTGAAGATTGGGGTGTTTTTCAGGTAATTGATCATGGGGTTGATGCTCAATTAATATCACAAATGACAAAATTAGCGAAGGAATTTTTCGAATTGCCTCCTGAGGAAAAGCTTCGGTTTGACATGTCTGGTGGCAAGAAAGGTGGCTTCATTGTCTCAAGCCACTTACAGGGTGAAGTGGTTCAAGACTGGCGTGAAATAGTGACTTACTTTTCATACCCCATTCGAGCTAGAGACTATTCTAGATGGCCAGACAAACCACAAGGCTGGATAGGTGTAACTGAGCAATACAGTGAAAAGTTGATGGATTTGGCTTGCAAATTATTAGAAGTACTATCAGAGGCAATGGGCTTAGAGAAAGAGGCTTTAACCAAGGCATGTGTCGATATGGACCAAAAAGTAGTTGTGAATTTTTACCCAAAGTGTCCAGAGCCTGACCTTACTCTTGGGCTCAAACGACACACCGATCCAGGAACCATTACCTTATTGTTACAAGACCAAGTTGGTGGGCTTCAAGCCACTAAAGATAATGGCAAAACATGGATCACTGTTCAGCCCGTTGAAGGTGCTTTTGTGGTTAATCTTGGCGATCACGGTCATTATTTGAGCAATGGAAGGTTCAAGAATGCTGATCATCAAGCAGTGGTGAATTCGAATAGCAGTAGATTATCGATAGCCACATTCCAGAATCCAGCACCAGATGCAAAAGTGTATCCGTTAAAAATTAGAGAAGGAGAGAAGTCAATAATGGATGAGCCGATTACATTTGCAGATATGTACAGGAGGAAAATGAGTAAGGATCTTGAGCTAGCTAGGCTGAAGAAACTGGCCAAGGAAGAGAAGATACAA------------ACTGAAGAGGCCAAGTTGGAGTCCAAGCCCATTGAGGAAATTCTTGCTTAA
	Solanum_tuberosum_AY102035            ATGGCT---TCAACACTAACAGCTCTAGCTAATGAAAAGACCCTTCAAACAAGTTTTATTAGGGATGAAGAAGAACGTCCAAAAGTGGCTTACAATAAATTTAGTGACGAAATTCCAGTAATATCGTTGCAAGGTATTGATGAT---------ATTAAT---GGAAGAAGAAGTGAAATATGTGAGAAAATTGTAAATGCTTGTGAAGATTGGGGAGTTTTTCAGGTAATTGATCATGGGGCCGATGCTCAATTAATATCAGAAATGACAAAATTGGCTAAGGAATTTTTCGAATTGCCTCCTGACGAAAAGCTTCGGTTTGACATGTCTGGTGGCAAGAAAGGCGGCTTTATTGTCTCAAGCCATTTACAGGGTGAAGTGGTTCAAGACTGGCGTGAAATAGTGACCTACTTTTCTTACCCAATTCGAGCTAGAGACTACTCCAGATGGCCAGACAAACCACAAGGCTGGATAGCTGTAACTGAGAAATACAGTGAAAAATTAATGGACTTGGCTTGCAAATTATTAGAAGTATTATCAGAGGCAATGGGCTTAGAGAAAGAGGCTTTAACCAAGGCATGTGTGGATATGGACCAAAAAGTAGTTGTCAATTTTTACCCAAAGTGTCCAGAGCCTGACCTTACCCTTGGGCTGAAACGACATACTGATCCAGGAACCATCACCCTCTTGTTACAAGACCAAGTTGGTGGGCTTCAAGCCACTAAAGATAATGGCAAAACTTGGATCACTGTTCAGCCCGTTGAAGGCGCTTTTGTTGTTAATCTTGGTGATCATGGTCATTATTTGAGCAATGGGAGGTTCAAGAATGCTGATCATCAAGCAGTTGTGAATTCGAATAGCAGCAGATTATCGATAGCCACTTTTCAGAATCCAGCACCGGATGCAAAAGTGTATCCGTTAAAAATTAGGGAAGGAGAGAAGGCAATAATGGATGAGCCGATTACATTTGCAGAAATGTACAGGAGGAAAATGAGTAAGGATCTTGAGCTTGCTAGGCTCAAGAAACTGGCCAAGGAACAG---------------------ACTGAAGAGGCCAAGTTGGAGTCCAAGCCCATTGAGGAAATTCTTGCTTAA
	Iochroma_cyaneum_KJ094352             ATGGCACCTTCAACACTAACGGCTTTGGCAGATGAAAAGACCCTCCAAACAAGTTTCATAAGGGATGAAGAAGAGCGTCCAAAAGTGGCATACAACAAATTCAGTGACGAGATACCAGTCATATCGTTGAAGGGACTTGGTGAG---------------AGTGGAAAAAGAGGTGAAATATGTGAAAAGATTGTAAAGGCATGTGAAGATTGGGGGGTTTTTCAGGTAGTTGATCATGGGGTGGATGATGAATTAATCTCACAAATGACAAAATTTGCTAAAGAATTCTTCGCGTTGCCTCCTGAGGAGAAGCTCCGGTTTGATATGTCTGGTGGCAAGAAAGGTGGCTTCATTGTCTCTAGCCATCTACAGGGTGAAGTGGTCCAAGACTGGCGTGAAATAGTGACTTATTTCTCATACCCAGTTGGGGCTAGAGATTACTCTAGATGGCCAGACAAACCACAAGGATGGATAGCTGTAGCTGAGAAGTACAGTGAAAAGTTAATGGACTTGGCTTGCAAATTACTAGAAGTATTATCAGAAGCAATGGGCTTGGAGAAGGAGGCCTTAACTAAGGCATGTGTGGATATGGATCAAAAAGTGGTTGTCAATTTTTACCCAAAGTGTCCACAGCCTGACCTTACCCTTGGGCTGAAACGACACACTGATCCAGGAACCATTACCCTCTTGTTACAAGATCAAGTTGGTGGGCTTCAAGCCACTAAAGATAATGGCAAAACATGGATCACTGTTCAGCCTGTTGAAGGCGCTTTTGTTGTCAATCTTGGTGATCATGGTCATTATTTGAGCAACGGGAGGTTCAAGAACGCTGATCATCAAGCAGTGGTGAACTCGAATAGCAGCAGATTATCGATAGCCACTTTCCAGAATCCAGCACCGGAGGCAATAGTGTATCCATTAAAAATTAGGGAAGGGGAGAAGGCAGTAATGGATGAGCCCATAACATTTGCAGAAATGTACAGGAGGAAAATGAGTAAGGATCTTGAGCTTGCTAGGCTCAAGAAACTGGCCAAAGAACAACAGATTCAA---------GCTGCTGAAAAGGCCAAGTTGGAATCCAAGCCCATTGAGGAAATTCTTGCTTAA
	Iochroma_calycinum_KJ094347           ATGGCACCTTCAACACTAACGGCTTTGGCAGATGAAAAGACCCTTCAAACAAGTTTCATAAGGGATGAAGAAGAGCGTCCAAAAGTGGCATACAATAAATTCAGTGACGAGATACCAGTCATATCGTTGAAGGGGCTTGGTGAG---------------AGTGGAAAAAGAGGTGAAATATGTGAAAAGATTGTAAAGGCATGTGAAGATTGGGGGGTTTTTCAGGTAGTTGATCATGGGGTGGATGATGAATTAATCTCACAAATGACAAAATTTGCTAAAGAATTCTTCGCGTTGCCTCCTGAGGAGAAGCTCCGGTTTGATATGTCTGGTGGCAAGAAAGGTGGCTTCATTGTCTCTAGCCATCTACAGGGTGAAGTGGTCCAAGACTGGCGTGAAATAGTGACTTATTTCTCATACCCAGTTGGGGCTAGAGATTGCTCTAGATGGCCAGACAAACCACAAGGATGGATAGCTGTAACTGAGAAGTACAGTGAAAAGTTAATGGACTTGGCTTGCAAATTACTAGAAGTATTATCAGAAGCAGTGGGCTTGGAGAAGGAGGGCTTAACTAAGGCATGTGTGGATATGGATCAAAAAGTGGTTGTCAATTTTTACCCAAAGTGTCCACAGCCTGACCTTACCCTTGGGCTGAAACGACACACTGATCCAGGAACCATTACCCTCTTGTTACAAGATCAAGTTGGTGGGCTTCAAGCCACTAAAGATAATGGCAAAACATGGATCACTGTTCAGCCTGTTGAAGGCGCTTTTGTTGTCAATCTTGGTGATCATGGTCATTATTTGAGCAACGGGAGGTTCAAGAACGCTGATCATCAAGCAGTGGTGAACTCGAATAGCTGCAGATTATCGATAGCCACTTTCCAGAATCCAGCACCGGAGGCAATAGTGTATCCATTAAAAATTAGGGAAGGGGAGAAGGCAGTAATGGATGAGCCCATAACATTTGCAGAAATGTACAGGAGGAAAATGAGTAAGGATCTTGAGCTTGCTAGGCTCAAGAAACTGGCCAAAGAACAACAGATTCAA---------GCTGCTGAAAAGGCCAAGTTGGAATCCAAGCCCATTGAGGAAATTCTTGCTTAA
	Iochroma_calycinum_KJ094358           ATGGCACCTTCAACACTAACGGCTTTGGCAGATGAAAAGACCCTTCAAACAAGTTTCATAAGGGATGAAGAAGAGCGTCCAAAAGTGGCATACAACAAATTCAGTGACGAGATACCAGTCATATCGTTGAAGGGGCTTGGTGAG---------------AGTGGAAAAAGAGGTGAAATATGTGAAAAGATTGTAAAGGCATGTGAAGATTGGGGGGTTTTTCAGGTAGTTGATCATGGGGTGGATGATGAATTAATCTCACAAATGACAAAATTTGCTAAAGAATTCTTCGCGTTGCCTCCTGAGGAGAAGCTCCGGTTTGATATGTCTGGTGGCAAGAAAGGTGGCTTCATTGTCTCTAGCCATCTACAGGGTGAAGTGGTCCAAGACTGGCGTGAAATAGTGACTTATTTCTCATACCCAGTTGGGGCTAGAGATTACTCTAGATGGCCAGACAAACCACAAGGATGGATAGCTGTAACTGAGAAGTACAGTGAAAAGTTAATGGACTTGGCTTGCAAATTACTAGAAGTATTATCAGAAGCAGTGGGCTTGGAGAAGGAGGGCTTAACTAAGGCATGTGTGGATATGGATCAAAAAGTGGTTGTCAATTTTTACCCAAAGTGTCCACAGCCTGACCTTACCCTTGGGCTGAAACGACACACTGATCCAGGAACCATTACCCTCTTGTTACAAGATCAAGTTGGTGGGCTTCAAGCCACTAAAGATAATGGCAAAACATGGATCACTGTTCAGCCTGTTGAAGGCGCTTTTGTTGTCAATCTTGGTGATCATGGTCATTATTTGAGCAACGGGAGGTTCAAGAACGCTGATCATCAAGCAGTGGTGAACTCGAATAGCTGCAGATTATCGATAGCCACTTTCCAGAATCCAGCACCGGAGGCAATAGTGTATCCATTAAAAATTAGGGAAGGGGAGAAGGCAGTAATGGATGAGCCCATAACATTTGCAGAAATGTACAGGAGGAAAATGAGTAAGGATCTTGAGCTTGCTAGGcTCaAGAAACTGGCCAAAgaacaacagattcaa---------gctgctgaaaaggccaagttggaatccaagcccattgaggaaattcttgcttaa

;



END;

BEGIN TREES;
	Title F3H_Tree;
	LINK Taxa = Taxa;
	TRANSLATE
		1 Petunia_hybrida_AF022142,
		2 Nicotiana_benthamiana_V0.4.2Scf2714_,
		3 Solanum_lycopersicum_HQ008775,
		4 Solanum_tuberosum_AY102035,
		5 Iochroma_cyaneum_KJ094352,
		6 Iochroma_calycinum_KJ094347,
		7 Iochroma_calycinum_KJ094358;
	TREE 'F3H Tree+' = (1:0.073273,2:0.054559,((3:0.041111,4:0.014368):0.05241,(5:0.001923,(6:0.001833,7:0.003999):0.003679):0.037243):0.028977);

END;


BEGIN CODONS;
	CODONPOSSET * UNTITLED  =  1: 1 - 1111\3, 2: 2 - 1112\3, 3: 3 - 1113\3;
	CODONPOSSET CodonPositions  =  1: 1 - 1111\3, 2: 2 - 1112\3, 3: 3 - 1113\3;

	CODESET * UNTITLED   =  universal:  1 -  1113;


END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  unord:  1 -  1113;

END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  'Jukes-Cantor':  1 -  1113;
END;

Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		timeSaved 1408739119020;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 3209408305193110551;
			tell It;
				setSelected  1;
				setDefaultOrder  4 3 5 6 2 0 1;
				attachments ;
			endTell;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 1567778487948929564;
			mqVersion 275;
			checksumv 0 3 3418106101 null  getNumChars 1113 numChars 1113 getNumTaxa 7 numTaxa 7   short true   bits 1152921504606846991   states 15   sumSquaresStatesOnly 161754.0 sumSquares -9.2233720368546243E18 longCompressibleToShort false usingShortMatrix true   NumFiles 1 NumMatrices 1 errorReportedDuringRun;
			mqVersion;
		endTell;
		getWindow;
		tell It;
			suppress;
			setResourcesState false false 174;
			setPopoutState 400;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 1258 478;
			setLocation -29 22;
			setFont SanSerif;
			setFontSize 10;
			getToolPalette;
			tell It;
			endTell;
			desuppress;
		endTell;
		getEmployee  #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
		tell It;
			showDataWindow #1567778487948929564 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					getTable;
					tell It;
						rowNamesWidth 178;
					endTell;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 1084 411;
					setLocation -29 22;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
						setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
					endTell;
					setActive;
					setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
					colorCells  #mesquite.molec.ColorByAA.ColorByAA;
				tell It;
					emphasizeDegeneracy off;
				endTell;
					colorRowNames  #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor;
					colorColumnNames  #mesquite.charMatrices.CharGroupColor.CharGroupColor;
					colorText  #mesquite.charMatrices.NoColor.NoColor;
					setBackground White;
					toggleShowNames on;
					toggleShowTaxonNames on;
					toggleTight on;
					toggleThinRows on;
					toggleShowChanges off;
					toggleSeparateLines off;
					toggleShowStates on;
					toggleAutoWCharNames off;
					toggleAutoTaxonNames off;
					toggleShowDefaultCharNames off;
					toggleConstrainCW on;
					toggleBirdsEye off;
					toggleShowPaleGrid off;
					toggleShowPaleCellColors off;
					togglePaleInapplicable on;
					toggleShowBoldCellText off;
					toggleAllowAutosize off;
					toggleColorsPanel off;
					toggleLinkedScrolling on;
					toggleScrollLinkedTables off;
				endTell;
				showWindow;
				getWindow;
				tell It;
					forceAutosize;
				endTell;
				getEmployee #mesquite.charMatrices.ColorByState.ColorByState;
				tell It;
					setStateLimit 9;
					toggleUniformMaximum on;
				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.SequenceInfoEditor.SequenceInfoEditor;
				tell It;
					panelOpen false;
				endTell;
			endTell;
		endTell;
		endTell;
end;