#NEXUS
[written Fri Dec 15 00:46:51 SGT 2017 by Mesquite  version 3.3 (build 854) at 179-139.priv23.nus.edu.sg/172.23.179.139]

BEGIN TAXA;
	TITLE Taxa;
	DIMENSIONS NTAX=8;
	TAXLABELS
		Gossypium_raimondii_GrLyk1 Gossypium_raimondii_GrLyk2 Gossypium_raimondii_GrLyk3 Gossypium_raimondii_GrLyk4 Gossypium_raimondii_GrLyk5 Gossypium_raimondii_GrLyk6 Gossypium_raimondii_GrLyk7 Gossypium_raimondii_GrLyk8 
	;

END;


BEGIN CHARACTERS;
	TITLE  Fig.S1A_Lyks;
	DIMENSIONS  NCHAR=751;
	FORMAT DATATYPE = Protein GAP = - MISSING = ?;
	MATRIX
	Gossypium_raimondii_GrLyk1  ---MLITMVSLSHHLLACLSLPLL--------VTLLVRICKADD-----MYPFPCSQEIQK--CDAFLYHTNTG---LDEVEIASYYSVDPSTFRPISHGNNKD---------YLIPVPCSCGDTDNGT-QAYFYDVYYTVKEG-DTFRNVSARFYNGQA-------LEVGGEENNFPTGSKVTMHLICGC-----LESQSTTVVTYTVQQGDSLSSMATQLSTSINDIQSLNRNL--TSNPDFINSGWVLYVPMAKDRIPAVP-----------------------KRKGGI---KWTIIIVILSAVTLFSMIALLIILVRRKAQQ-------MSEEDPKPVSKSISARAFSL-------------------QNSFLYKDNIE--------DVTAFESDRPMIYSLEEIEEATDNFDETKKIGTGGYGYVYHGILGAKEVAVKKMKSSKSKEFFAELKVLCKVHHINVVELLGFASG--DDHLYLVYEFVQNGSLNDHLHE----PLL---KGHQPLSWTARAQIALDAAKGIEYIHDHTKARYVHRDIKTSNILLDKGLRAKVADFGLAKLVERTN-EEDLLATRLVGTPGYLPPESVMELQVTPKTDVFAFGVVLAELITGQRALVRDNK---EPNKMRSLITVVNNVFE---EENPESALEEVIDGSL-RGSYPMEDAYKMAELAEWCLSDEAVNRPEMRDVVLTLSKIVMSSVE-----WEASLGGSSQVFSGVFNGR--------
	Gossypium_raimondii_GrLyk2  -----MDPKVSQFVILLPLISLLI--------VQTLNALDSSSA-----TIPMNCTDTSRL--CTSFLAFKPQGN--QSLAVIQSMFDVIPQDITVEGEDSHGY---------IFIKKNCSCLTTS----KNYATNTTFTVRSNQGYVYDMILEAYDGLA-------MVPN-VSRPARIGAVVSLRLFCGCSS-----SLWNYLMSYVMKDGDSVQSLASRFGVSMDSIEQVNGIS----NPDNVTVGALYYIPLNSAPGEPYHVENEIPPAPVPAPSADTISEIQVSPKAHVPY-GWIIGGLGV-GLALIILSIVVCVSLRSSSCFVEARGSHAKDHDDKSSHKFHILRKPSFCCGSGRYICGKSENWTQTNGEPSNHQITIPNA---LGTDVLD--VEKPVVFTYEDILFSTDGFSDSNLLGRGIYGSVYFGFLRDQEVAIKRMTATKTKEFMAEMKVLCKVHHANLVELIGYAAS--DNELFLIYEYAQKGSLRSHLHD----PLN---KGHTPLSWIMRVQIALDAARGLEYIHEHTKTHYVHRDIKSSNILLDGSFRAKISDFGLSKLVGKTN-DEEATATKVVGTFGYLAPEYLSDGLASSKSDVYAFGVVLFEIISGKEAIIRTEGSAMKNTERRSLASIMLAALRNTPDLLSISNMKDYIDPSM-LDLYPHDCVFKMAMLAKQCVDEDPIVRPDMKQVVINLSQILLSSVE-----WEATLAGNSQVFSGLVQGR--------
	Gossypium_raimondii_GrLyk3  ---MSKIYLRALVLLIWLLISPLG--------QNLLSCNVTSPD-----ALGYRCGINGSEDQCGTFAVLRATSY-YSSLSNLSFYLGFNRVAIAEANGFSAQTEFLPRDQP-LLLPIDCKCNN------GFFHADLTKTTIKG-ESFYGIA-ESLQGLTTCKAIQDKNPGVSPWGLGDKVRLVVPLRCACPSPSEVTLKARLLLSYPVSPGDTISNLAAAFNTTSEAIISANNRSLETFEPESLATLTSLLIPLNGEPLPHFP----------E--TSIPIINPQKKKPRMWKAGVYIAVSGVVIGTIIAVAATFLVIRLKRKKKKQN-----LSKDDDLELQQLSLSVRTAS-------------------EKKVSFAGSQDAGDGPLIDSVTPR-KALLELYTIEELRKATEDFNPSTHIE----GSVYHGHLNGKNMAIRRTRTENISKVETRFFTDATHHHPNIIRLLGTCVT-EGSHPFLVFEYAKNGSLKDWLHGGLAMKNQFIASCYCFLTWKQRLKISFDIAVALQYMHQVMNPSYVHRNIKSRNIFLDEDLNAKIGNFGMARCVEDDTKYPDLSTNPSSWSLGYLAPEYLHQGVISPGIDIFAYGIVLLEILSGQTPISRPDK---KGGGNVWLSEKIKAIL----QSESADELRAWMDSAL-GENYSFDTAVTLANLARACTEEDPCLRPSAGEIVDRLSRLVEESTE-----GEHTLIFESSSK--PLVNTSSTTSNL-
	Gossypium_raimondii_GrLyk4  ------MRTKLSYVFVFCLLFFVF-------------HANSQPS-----TTGYTCNLNQTTYPCQTYVFFRATAPNYLDLASIGDLFNISRLMISEPSNISSPSAPLIPDQF-LFVPISCACNSINDTIGSLSAANLTYTFIRG-DTFYRVSTLNFQNLTTYQSVEVFNPDAVPTQIEIGQRIVFPIFCKCPNETQIRNGVKYLVSYVYQPLDNLSVIASRFGIQTQAITGANNDS--------IQPYDTIFIPVSRLPVLSQP-------------EPAPVASGKTERTGVI---IGLSIGLGICGILMILL--FVVLVYREVLSGRRG----KERDEENHRLKM---------------------------NRPGMGVKGIEAN---LMADVSGC-LDKYRVFKIEELREATDDFSDSCLIQ----GSVYKGSIDGDNYAIKKMKWNASEE----LKILQKVNHGNLVKLEGFCIDPEDTSCYLVYEFIENGSLSFWLHE----------NDNEKLSWRTRLRIAVDVAHGLQYIHEHTRPRVVHKDIKTSNILLDANMRAKIANFGLAKS------GCNAITVHIVGTQGYIAPEYLADGVVSTKMDVFSFGVVLLELVSGKEAI---------DEEVRLLWASVEGVLDGN-EERKERQVREFMDGCLLEQSLSMEGVMNVMAVAISCLNKDPTKRPSMVDIVYALSKSD--DLV-----FDESEDSLSAP---PVVAR--------
	Gossypium_raimondii_GrLyk5  ----MRIKPHQQVFFSWFLILFLF------------HGSQTQPS-----TTGYTCTPNQTTYPCQTYVFYRATAPNFLDLASIGDLFHVSRLMISQPSNISSPSSLLIPYQS-LFVPITCSCNSVTATFGSLSAANLTYTIKGG-DTFYLVSTRNFQNLTTYQSVEVFNPSSVPTRLKIGGEIVFPIFCKCPNETQAKTGVNYLVSYVFQPYDNLSLVASRFGVRTHDINNMNGNK--------IHPFDTIFIPVNKLPVLPQP------------KAPSAASPGNAEKKRAI---VGLAIGLGICGVLLIFF--FAVLLYRDVFSKKRD----MERPEDNQKIQF---------------------------NRPGMLMKGNEVN---LMADVSDC-LDMYRVFNIEELREATDCFNESCLIQ----GSVYKGSINGGTYAIKKMKWNACEE----LKILQKVNHGNLVKLEGFCIDPEDTTCYLVYEFIENGCLYSCLHQ----------NNNGKLNWKTRLRIAVDVANGLQYIHEHTRPKVVHKDIKSGNILLDSNMRAKIANFGLAKS------GCNAITMHIVGTQGYIAPEYVADGVVSTKMDVFSFGVVLLELVSGREAI---------GEGGKLLWGSVNGVLDGS-EERKVKKVKEFMDGGLEGGGCWMESVMNVMGIAIACVNKDPRRRPRMVDVVYALSMTH--DLF-----FHVSEDGLSP----PLFPR--------
	Gossypium_raimondii_GrLyk6  MAISFLSHQWQSLQVVFFVLNYVF--------ASYIRAQPSSSN-----GADFWCSRSSAP--CPTYTAYFAQEPDYLDLQNIAKLFGTSPQEIARASNLVSEDTRLFPGQL-LLVPIICGCTR------NHYFANITYDIKFG-DTYYIVSTTVFEHLTNFTTVGDMNPSLDPKSLQVGDKVVFPLFCKCPSKAELKNETEYFISYVWQPNDDIWSVSAKFNASAPAIIDENKLN--DYQDISLAVIPPLMIPVSDLPVLLQT----------------QFSGGSKSKHR-----GGLIVVLSIVGCLLVLA---GVVIHKRKKVFRRN----GWSPETVGLIPVKDLTKSES-------------------FQPKIIQDK-------LLPGVSGY-LGKPIMYEAHVIMGATMNLNEHCRIG----GTVYRATIDGKLLAIKKTKDDITKE----LKILQKVNHANLVKLMGVSAD-SDGNCYLVYEYAENGSLDKWLHP----KSSCSSSRAAVLTWSQRLQVALDVANGLQYMHEHTQPNIVHRDIRTSNILLDSTFKAKISNFSVTETIAN---------------------------AIMPKVDVFAFGVVLLELLSGKKAMTTK-----ENGEIFMLWKQIRQVLEI--EEKREKRLRKWMDPNL-ESFYPLDSALSLAVLAMACTQENPLARPSMAEIVFSLSVLIQSSFEISEGSWGSGIETELDQMIVPVVAR--------
	Gossypium_raimondii_GrLyk7  -MAVGRLKPCLKFCLPFLLLFFLGFTQAQQGYVNNLQLACEDPTKDNNISRGFSCNGEQRS--CQSYITFRSEPPFYNTAVSIAYLLDAQATQISSLNNLSADVSSITPKSM-VVVPVNCSCSGTVND--SYYQHNASYTMKFDYETYFSISNDTYQGLTTCQAMKAQNPI-DYRNLEVGNKLVVPIRCACPTYNQIRAGAKYLLSYIVTWGDSISSIAETFGADEKSVLEANELS----EDDIIFPFTPVLVPLSEEPSMIKPPQSSPPPASVPQIPTSPVGESDSKSSKKW---VFIGVGVGIGSLLLLGLAGFLFCFFRRQRQAHKARPIAAASPPPMPPFNLKPFSDSTN-------------------YTPNSWSVSISSQ------GVRHA-IESLTRYKFEDLKAATGNFGESNRIK----GSVFRGSFQGDDAAVKVMKGDVSSE----INLLKKINHTNIIRLSGFCVH--EGNTYLVYEYADKGSVSDLLHS----NKF---QSSFTLSWKQRVQIAYDVADALNYLHNYINPPYIHKNLKSSNILLDVNFRAKVTNFGLARTIEDNDEGGLQLTRHVVGTKGYMAPEYIENGVITPKLDVFALGVIILELLSGEDAANAE-----KNGGEELLSASIRVVLE---GDNVREKLKNFIDPSL-GPEYPLDLAFSMAQLAKICVAHDLNARPSMADVLVTLSKILSSSLD-----WDPSSEFERSTS--LTSAR--------
	Gossypium_raimondii_GrLyk8  -----MDQFRFGFFILLCVFMHKFHAQQSYSGNSILNCSENDETGSSS-AFLYTCNGEKPS--CQAFLIFKSYPP-YDSISTISNLTSADPLELAHINNISLST--IFPANKEVIVPVNCSCSG------QYYQANTSYIIPSKQVDYFSIANNTYQGLSTCKS---LNKENSDSGLQAGSVLQVPLRCACPTRNQTLNGIKFLMTYVVHWEDTIHDISKRFNASMESVGDANGID---LDDALIFPFTTVLVPLSTKPSSSQT--IIHFQQPPASSPTTPIDVIKSSRKRFT---VWLAIGVPLLALFLLLL--LMFLHHKKTRE--------AARKDKRKKWEL-----------------------------PNDVLVSIDQN---------------LKVYDFKDLEAATENFSNKYKMG----ASVYRGVLKGELLAIKQMSKAVDKE----VSLLQRINHFNLISLRGACEH--SGVFYLVYEFMENGSLKEWLQN---------KSCQKFQHMCIKIFVVTTLARSAE-----------REDSRKSSMW------------------------------SSLGTKGYKAPEYIEYGLVTPEMDIYAFGVLLLELITGKPAVFM------QDEKEVLLSERILTIMK---GENADAEIDHIIDPNL-KGHLWMKLARQMLKLSIDCLAEEPESRLSMAEVVSYLLRI---QLD-----AQRSEE----PF--PSEWR--------

;


END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  unord:  1 -  751;

END;

BEGIN NOTES;

	TAXABITS   NAME = newlyAddedTaxon on =  1 -  8;

END;

BEGIN CODONS;
	CODESET * UNTITLED   =  universal:  1 -  751;


END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  'Mk1 (est.)':  1 -  751;
END;

BEGIN TREES;
	Title Fig.S1A;
	ID 015de8e1ec437;
	LINK Taxa = Taxa;
	TRANSLATE
[0] 		1 Gossypium_raimondii_GrLyk1,
[1] 		2 Gossypium_raimondii_GrLyk2,
[2] 		3 Gossypium_raimondii_GrLyk3,
[3] 		4 Gossypium_raimondii_GrLyk4,
[4] 		5 Gossypium_raimondii_GrLyk5,
[5] 		6 Gossypium_raimondii_GrLyk6,
[6] 		7 Gossypium_raimondii_GrLyk7,
[7] 		8 Gossypium_raimondii_GrLyk8;
	TREE Fig.S1A = (((((4,5)[%posteriorProbability = 1 ],6)[%posteriorProbability = 0.988 ],(7,8)[%posteriorProbability = 0.944 ])[%posteriorProbability = 0.436 ],3)[%posteriorProbability = 1 ],(1,2)[%posteriorProbability = 1 ])[% ] [% ] [%  setBetweenDouble = posteriorProbability ];

END;


Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		timeSaved 1513270011987;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 1180750125450895580;
			tell It;
				attachments ;
			endTell;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 1028970945896529242;
			mqVersion 330;
			checksumv 0 3 2465532116 null  getNumChars 751 numChars 751 getNumTaxa 8 numTaxa 8   short false   bits 1048575   states 1048575   sumSquaresStatesOnly 6.0328859060132E13 sumSquares 6.0328859060132E13 longCompressibleToShort false usingShortMatrix false   NumFiles 1 NumMatrices 1 errorReportedDuringRun;
			mqVersion;
		endTell;
		getWindow;
		tell It;
			suppress;
			setResourcesState true false 100;
			setPopoutState 300;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 917 495;
			setLocation 394 67;
			setFont SanSerif;
			setFontSize 10;
			getToolPalette;
			tell It;
			endTell;
			setActive;
			desuppress;
		endTell;
		getEmployee  #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
		tell It;
			showDataWindow #1028970945896529242 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 0 -72;
					setLocation 394 67;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
						setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
					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;
					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;
				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 8 3 2 2;
					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;