#NEXUS
[written Wed Sep 20 17:36:21 PDT 2017 by Mesquite  version 3.31 (build 859) at howards-imac.dyn.ucr.edu/138.23.59.190]

BEGIN TAXA;
	TITLE Taxa;
	DIMENSIONS NTAX=19;
	TAXLABELS
		Pythium_ultimum Theileria_parva Babesia_bigemina Plasmodium_vivax Toxoplasma_gondii Eimeria_tenella Deinococcus_misasensis Capsaspora_owczarzaki Crassostrea_gigas Arabidopsis_thaliana Populus_trichocarpa Solanum_lycopersicum Myxococcus_virescens Pythium_arrhenomanes Pythium_irregulare Homo_sapiens Gallus_gallus Tetrahymena_thermophila Gekko_japonicus 
	;

END;


BEGIN CHARACTERS;
	TITLE  Character_Matrix;
	DIMENSIONS  NCHAR=231;
	FORMAT DATATYPE = Protein GAP = - MISSING = ?;
	MATRIX
	Pythium_ultimum          ------PGID------YLGAGYDLVFGNPDGSTDPGFRVHIIKFTWSNWTCPNELTILPQTSCMQQSSSSKIESTKSFQQVLQKDAKVTAFSGSRTMATMAVCVEYSATLPLAQFSSAVAELPLMYIKYFRFIQLFGTHYTTKVEMGGKIIHRVEIKQSDVSVMEVGGSDDWREWAKSTMDTPMPIRYTLTSLVDLVAFEQAVADYIAAYGR-------------------
	Theileria_parva          NSIGDDPDVE------YLGSGYDIIFGNPLGDMDQGYRNPVIRLNWEDLKEPRGSWIRPEYSCRQSETIDHVNTVDDFKKELSVDAQASSFSASTGYKNFTYCLRYVGGITTDEFKKAVEALPDKFLPWMQFIKMFGTHFTTIVHLGGKITHQVQIDKSDVLHMQIGGDNSLNNWAKELYKRPMPIKIKLESIKSLL-FDEALKFYSETYGV-------------------
	Babesia_bigemina         ------AAIR------YLGSGYDIVFGNPLGDVDPGYRDPVLKLDWTELKEPRGGWIRPELSCRQAETVDHVNTIEDYKKELSVDAKISGFSASGGYKTFTYCLRYVAGIPMPSFKNDVEELPEKFHPWIKFFKKYGTHYTTVIHLGGKVTNQIQMKKTDVAAIQIGGDVSMQEWTRSLYRKPMPIKVNLDSIKTLIEFDVALKYYSELYGI-------------------
	Plasmodium_vivax         ------QGTE------YLGVGYDFIFGNPIGDVDPGYRDSIIKLTYPKNINPNGSYVRNEISCNRSENESEISTMSEYTKELSVDASIGSFSASTGYTSVSYCFKYMASLLSDQFVRAISLLPSYFESWMYFFKNFGTHVSTLIHLGGKITQQVKISKNEYKAMNIGGTKNFEKWAKSIKDNPMPIKGEYEPLSRIL-YEEALQFYISVNVP-------------------
	Toxoplasma_gondii        ------PAIN------YLGAGYDHVRGNPVGDGDPGIRPPVLRFTYAQVLQPLGGYVRQYVACRQSETISELSNLSDYQNELSVDASLQSFSASTGYRDFNYCMRYEAGVVTLAFAAGVSQLPDVFPIWISFIEQFGTHFLVRLFAGGKMTYQVTAKRSEVEKMRIGGRAALAAWADTVEELPMPVKFEVQPLYHLL-FKQAVTFYSKAVGL-------------------
	Eimeria_tenella          VHLAGAPASEPSDDEDFLGSGYNLVFGNPLGDGDPGFRAPVIAFDWGHTLQPKGGYIRPYVSCQSAETIEEIESLKDYVTDLTADAQVDPFSGSLNFRKIAYCIRYEAGFTTEAFNKAVAKLPSSFVQWMEFFSDFGTHVTTNIKLGGKITKQIRVLKEHAQDL-VGGRQELSQWEKSVAALPMPVQYQLQPLTRLL-YRSASSFYSQAFGY-------------------
	Deinococcus_misasensis   ------PNIE------FLGRGYDLLLTDPLD-ASSGVKATVIALQYQKFRFPDGTQNAPDPGGTTSLTFQQMFRQTDYQSQFGETATISKFSLSESYSQS-YTVNFTPALMDTDFANAVGNLSSAS-TYQQFIQQFGTHYSTSVGFGGRAYQYTVVEATTFSSMVSGGRDDWDHWVSSVVDQPVPIALTLAPLSDLLALETAISNYLQANGA-------------------
	Capsaspora_owczarzaki    ------PNIA------YLGRGYDVVRGNPQSTVDPGIRASIMVLEHAEFYVPDNVDVIMEPVNRFESSSKLVRSEQSYKTMLESDLKIRSFSASESYQQVAETVSYRARLLTAEFRHAVQRLPALFSAYDDLLETFGTHYMHEVTMGGRGMQRFSIDMSEAATLDIGGETSLKDWARTVGSNPVPIRMQVAPIIELLPLASYLASYCESVSGDKVKFTRENNNTTLPFYGN
	Crassostrea_gigas        -------NLG------YIGRGYDLFKGNPLTDVDQGFRLPIMELPYTHYRIPDNVDVISESSAKFGSSLHTVQSESDYKKMLSVDASVNSFSASASYQKNSRAVVYRARMVNDYFEKAVMLLPMEDEMYINLVREFGTHYTTEVVMGAKAVQQLTFSKSDLSKLEIGGNESLREWARSADEKPVPIQYKMSSIESLL----------------------------------
	Arabidopsis_thaliana     -------AIQ------ALGRGFDVTSDVRLL-GAPGSR--LVRIEEGQFLLPNVPADIDCSRGNSGTQRISVCSFHEMAEEFNVRSGVKCFNAMFNYTGSYFIPLYDVKLLHNEIRRAV---PSSWASLASFIENYGTHIVTSVTIGGR--DVVYIRQHQSSPLP-GGDQSHARWAETVPAAPDIINMTFTPIVSLLELTRAIELYLEYKPP-------------------
	Populus_trichocarpa      -------SIQ------ALGRGFDVTSDIRLL-GATGSR--LVHIDDEHVVLPNVSFDIDCSKENRSIERIPVCSFHEMAGQFNEKSGISSFNGMFNFTGSHFIPLYKVQILLEEVKRAV---PSSWASLASFIESYGTHIVTSATIGGR--DVVYIRQHQASPLS-GGDQSHAKWAETVQLAPDVINMTFTPIVSLLELARAVDLYLEYKPP-------------------
	Solanum_lycopersicum     -------SIQ------ALGRGFDVTSDIRLL-GAPGSR--LVHLDEENILLPNVTVDIECSQELRTIEATPVFTFHEMAKYFNAISNIFSFNSMFNFTGSHVIPLFTVRLLRDEIKRAV---PYSWASLASFIENYGTHIVTSATIGGR--DVVYIKQHQSSPLL-GGDQSHDKWASTVETSPDVINMTFTPIVSFLELSRAIELYLEYKPP-------------------
	Myxococcus_virescens     -------NID------FLGRCYDVIRINPLDLGGGATTESIVQIPPESLYIPEGTRYLSESRGERTSRTQTWFSSFDFSHSFEHTVSAGSFSASLTYRQFSFFEDCSIELLSSRFTQEVAKL----NACAAFIKTFGTHYAREVTFGGRMYQRVHISSKEYSRFVVGGTTDFNEWVKSIRQDPKPLKLDLKPLYELFSMMQAVDTHIRTEGF-------------------
	Pythium_arrhenomanes     ------GTIA------WMSDWEQL--------AESG------------WTCPAEAAILPMASCLQQSSSDAISSTKSFQRVLQKDCSVASFSGSKAMASMAVCVDYVASLVLPDFAAAVNELPLSYVRFFRFIQLYGTHYTTRVEMGGKIIRRVEIKESDVQTLQIGGSEDWRLWAATTTADPMPIRYRLSPLVELVNFEQAVADYIAAYGK-------------------
	Pythium_irregulare       ------PGID------YVGAGYDLVFGNPDGSTDPGFRIHLIKFTWNDWTCPKELTIMPQTSCMQQSSSSMISSTKSFQQVLQKDAKVTSFSGSNAMSTMAVCVEYSASLTLVHFNSAVSELPLVYIKYFRFIQMFGTHFTTKVEMGGKIIHRVEIKQSDVSLLQVGGSEDWREWAKSTMDTPMPIRYTLTSLVDLIAFEQAVTDYISAYGR-------------------
	Homo_sapiens             ------PGAW------LAGEGVDVTSLRRSGSTQRFLRDGTCTLCENALPLALTNWRAQGSGCQRHVTRAKVSSTNDWKVGLDVTPKPTSHSQAANFAAQ--CRFYSFHVLHPDFKRALGDLPHHFPAYLRLISNYGTHFIRAVELGGRISALTALRTCELALEGVGGTEQYSAWVNSLPGSPGLVDYTLEPLHVLLDLRRALSQYLTDRAR-------------------
	Gallus_gallus            ------PGTD------IVGSGLDVTTMS-LTETKPTSRCVVCRLHEGRWRAGSKCRKRSSLATGRKSMKTLVSQTQNWKVGLRVALHPGSHSRVAEFGMQ--CVHYWISAPSSHFLHAVRSLPPHYPDYADLLAAYGTHYIHSAQLGGLLRSITAIRSCRAAMMGEGGEENYAKWLSSLQRLPGLVASIVRPLHTLLPLKAAVSHYIAWRAL-------------------
	Tetrahymena_thermophila  ------PNVQ------YLGSGYNIYFANPHSTLDPGFTSGILELDYNNYYVPDNVSLTVEKSCIVSFQSQEVNSLSQYRDSLSSSVQFQKFSASSDYQEVARCSIFQLDVLTPQLQQALFTL--AFNDYYDFIDTWGTHVVTSVNLGSRFGYKYQMDKYQSNQLTIGATQDPLSWAQQTLDTPMPINISILSFDDFLGVISNLSQYLQTYCA-------------------
	Gekko_japonicus          ------PGHN------LAGEGFDVTTLERKGAMTQWESDGTCNLC--QLPLAAADWEV-DVSCRRKLHSSLQESGNDWRMGLEVEVKPESHSKMADFSID--CVFYKFRILTQHFRRALKVLPAKYLEYHQLIETYGTHFITKLHLGGRVRDVTAIRECETVLDGVGGNEAFQEWAEGLKTMPGLVSYSLAPIHTLVALRQAVSEYVTRRAL-------------------

;


END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  unord:  1 -  231;

END;

BEGIN CODONS;
	CODESET * UNTITLED   =  universal:  1 -  231;


END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  'Mk1 (est.)':  1 -  231;
END;

Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		timeSaved 1505954181720;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 8151423559852124855;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 2991546392087098993;
			mqVersion 331;
			checksumv 0 3 2405940099 null  getNumChars 231 numChars 231 getNumTaxa 19 numTaxa 19   short false   bits 1048575   states 1048575   sumSquaresStatesOnly 5.8168289888627E13 sumSquares 5.8168289888627E13 longCompressibleToShort false usingShortMatrix false   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 1271 646;
			setLocation 8 22;
			setFont SanSerif;
			setFontSize 10;
			getToolPalette;
			tell It;
			endTell;
			desuppress;
		endTell;
		getEmployee  #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
		tell It;
			showDataWindow #2991546392087098993 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 1171 574;
					setLocation 8 22;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
					endTell;
					setActive;
					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;
					toggleAutoWCharNames off;
					toggleAutoTaxonNames off;
					toggleShowDefaultCharNames off;
					toggleConstrainCW on;
					toggleBirdsEye off;
					toggleShowPaleGrid off;
					toggleShowPaleCellColors off;
					toggleShowPaleExcluded off;
					togglePaleInapplicable on;
					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 16 6 1 1;
					subCosts  5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5;
				endTell;
				getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor;
				tell It;
					panelOpen false;
				endTell;
			endTell;
		endTell;
		endTell;
end;