NEXUS
[File created by TreeBASE:  7/26/07  21:09:56]
[Matrix accession#: M2512]

BEGIN TAXA;
	TITLE M2512;
	DIMENSIONS  NTAX=14;
	TAXLABELS
		MS2_Enterobacterio_phage_MS2	YFV_Yellow_fever_virus	OnuMV6_Ld_Ophiostoma_mitovirus_6	OnuMV5_Ld_Ophiostoma_mitovirus_5	OnuMV4_Ld_Ophiostoma_mitovirus_4	ScNV_20S_Saccharomyces_cerevisiae_narnavirus_20S_RNA	ScNV_23S_Saccharomyces_cerevisiae_narnavirus_23S_RNA	OnuMV3a_Ld_Ophiostoma_mitovirus_3a	CpMV1_NB63_Cowpea_mosaic_virus	Qbeta_Enterobacteriophage_Qbeta	CeMV_Celery_mosaic_virus	L_dsRNA_Sclerotinia_homoeocarpa_mitovirus	GaMV_S1_Galinsoga_mosaic_virus	RsM2_1A1_Rhizoctonia_solani_virus
	;
END;

BEGIN CHARACTERS;
	TITLE M2512;
	DIMENSIONS NCHAR=717;
	FORMAT DATATYPE = PROTEIN SYMBOLS = " 1 2 3 4 " MISSING = ? GAP = - ;
	MATRIX
		MS2_Enterobacterio_phage_MS2                               PTLGSGNDEATRRTLAIAKLREANGDRGQINREGFLHDKSLSWDPDVLQTSIRS---------------------------------------------------------------------------LIGNLLSGYR-----------------------SSLFGQCTFSNGAPMGHKLQDAAPYKKFAEQ-------ATVTPRALRAALLVRDQCAAWIRHAVRY--------NESYEFRLVVGNGVFTVPKNNKIDRAACKEPDMNMYLQKGVGAFIRRRLKSVGIDLNDQSINQRLAQQGSVDG--------SLATIDLSSASDSISDRLVWSFLP---------PELYSYLDRIRSHYGIVDG--------------ETIRWELFSTMGNGFTFELESMIFWAIVKATQIHFGNAG------TIGIYGDDIICPSEIAPRVLEALAY--YGFKPNLRKTFVSG--LFRESCGAHFYRGVDVKPFYIKKPVDNLFALMLILNRLRGWGVVG--------------------GMSDPRLYKVWVRLSSQVPSMFFGGTDLAADYYVVSPPTAVSVYTKTPYGRLLADTRTSGFRLARIAR---ERK-----------------------------------------------FFSEKHDSGRYIAWFHTGGEITDSMK----SAGVRVIRTSEWLTPVPTFPQECGPASSPR
		YFV_Yellow_fever_virus                                     LAVLRKVKRVVASLMRGLSSRKRRSHDVLTVQFLILGMLLMTGGVTLVRKNRWLLLNVTSEDLGKTFSVGTGNCTTNILEAKYWCPDSMEYNCPN--------------------------LSPREEPDDIDCWCYGVEN------------VRVAYGKCDSAGRSRRSRRAIDLPTHENHGLKTRQEKWMTGRMGERQLQKIERWFVRNPFFAVTALTIAYLVG-----------SNMTQRVVIALLVLAVGPAYSAHCIGITDRDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDISLETVAIDRPAEVRKVCYNAVLTHVKINDKCPSTGEAHLAEENEGD----NACKRTYSDRGWGNGCGLFG-----------KGSIVACAKFTCAKSMSLFEVDQTKIQYVIRAQLHVGAKQEN----WNTDIKTLKFDALSGSQEVEFIGYGKATLECQVQTAVDFGN--SYIAEMETESWIVDRQWAQDLTLPWQSGSGGVWREMHHLVEFEPPH------------------AATIRVLALGNQEGSLKTALTGAMRVTKDTNDNNLYKLHGGHVSCRVKLSALTLKGTSYKICTDKMFFVKNPTDTGHGTVVMQVKVSKGAPCRIPVIVADDLTAAIN-------KGILVTVNPIASTNDDEVLIEVNPPFGDSYIIVGRGDSRLTYQWHKEGSSIGKLFTQTMKGVERLAVMG
		OnuMV6_Ld_Ophiostoma_mitovirus_6                           VKYLKELRLHITKYISGE-PYRNSLNRVSVDKDGFP-TLCKELKVLVNGTYLEK------RFVLTIITLSKLLIPQ--KSESIPFSTKSITDHWSG--------------------------IDNISNEELDKSCSELN---------ISTREV------QWDVKNFKLLTKAGPHGPQSLTWYHTIKLYDFN--QWLGIIGILPKSVLDLFTETLSYASKLVLPEIK--------SNIKSTKLIR--RLSIVHDPECKERVIAIFDYGSQMVLKPIADVLFDLLRNIPSDRTFTQSPFFTHTDLDNKS--------KFWSIDLSSATDRFPIVFQKRVLQKILG-----KQMTDSWERIMIGSKFLAPD-----GDTVS----YNCGQPMGAQSSWPMFTLAHHVIVRVAANRCG-LSNFD------KYIILGDDIVINNDNVALKYMEIMN-DFKVEISRNKTHVS--NDTYEFAKRWIKNKMEFFPLPIRGIVDNINNKYIIFNILYSFFVEKGNTFLNKDTLLVCVSKFIQLHSLTLKKPIGLNKVKGILYPFNFMLRYRQNLCTNEEIR------IFLGSSTCKRDDYMLPISAKDVSL---ELTRVISAALVGMAYNAEKSLKNIYFDLDKLSPWIGDGFKTGKHPKVMIQSIYNSVKSLSDFGLKMAQNKLTLSAA----MDSLLLVDLDSISSSERIKYIQMKQNICLS
		OnuMV5_Ld_Ophiostoma_mitovirus_5                           IKYMKAVKLHITKYIANERLLSISGSRVSVDKDGFP-TKFNYIKHIIDSGDIDG-----IRFVMTLLTYTRAINPTKKEYLKIFPDYSTITNEFTGS------------------------NKIAIPNKIIKEFVDYYK---------LANPNNNNNPELQWSRDDHYLSFKSSPNGQSTLHSSYGLFSMIFV--GHTILENILKIVGEKQYHEIIGNHIKKLYHDHR--------LFIPGKIDYLFGKISIVKDPELKMRVIAMVDYHSQFVLKKIHNSLFNKLKLIKSDRTFTQD-PIFTT-PTMGH--------RFWSMDLSAATDRFPIDLQERLLSYLYG-----SEISSAWKQLLIDRTYKTPE-----GDE----LHYKVGQPMGAYSSWAAFTLTHHLVVFYSARMAG-IKDFT------NYILLGDDIVINNDKVAKYYIRTMK-RLGVELSMNKTHVS--KNTYEFAKRWFKNKKEITGLPLRGILNNLNNYGIVFQELFKFHYK--YPHLTNVKLTDIMFIIFKGLKIKGRI-ITNSQLRFNLMKINFLLRYINKLVNFDETRLFYTKFIKSEDISMVNEHNFLDFTRGMLKL---GLTQKIENS----VKELKTFYDDVLKNSFISNIE---NKNDLQYEPLINGLYNKMLIMRNSIDRIVRNKDFDIIDA----MNDMRLDNPEAYLEKIKNSNKPLSNLNDMF
		OnuMV4_Ld_Ophiostoma_mitovirus_4                           IKYMKAAKLHITRYMCGKPLYSNN-ENVALDKTGFP-LRFWYLKRLVNDNP---------RALLTLLTYTRRIVPNKSESKARIVKLSTITDPYKG-------------------------KVYTIPKWFILDFISKYN---------LSSTKP------IYTDNDHYLSIKGSPNGKASMSSLYSIISFNSS--NIRYLFNIVG----DYQLVLN--KFYQDLSQFY--------TKYINRDKLGLGKLSIVHDPELKERVIAMVDYTTQFALRPIHNILLNNLSKLPCDRTFTQD-PFHKWNDDHKE--------RYHSLDLSAATDRFPIFLQQKLISLIFND----YEFGKNWRNLLVDRNYDY-------QGIS---YRYSVGQPMGAYTSWAAFTLTHHLVVHWAAELAG-LKNFK------DYIILGDDIVIKNNKVAQIYINLMT-KWGVDISLSKTHVS--YDTYEFAKRWIKNGKEISGISLKGILTNIRHIHVVYMNIFTYLQR--IPS-LNVDILTCVGKLYGYLLIRNRI-KSPNTIKRSLYDFHHSIRYSFGLLNYEEIRNYLHNKFPFDNYYAWPERLVHSKLNEIFKL---EMVESAKSFSKDFMNQSTMLINTVTDNEIM-----------VQW-PLYKGFMNHIEKLKDYIKSKQNQHDIDLLDL----MQNLRFQNLDSIVKKLRNSYTNLIMLDKFW
		ScNV_20S_Saccharomyces_cerevisiae_narnavirus_20S_RNA       GVVVSRGTRSLPPSLRLFRAMTRKWLSVTARGNGVEFAIASAKEFSAACRAGWISG----TVPDHFFMKWLPEPVRRKSGLWAQLSFIGRSLPEGGD-----------------------RHEIEALANHKAALSSSFEVP-------ADVLTSLRNYSEDWARRHLAADPDPSLLCEPCTGNSATFERTRREGGFAQSITDLVSSSPTDNLPPLESMPFGPTQGQALPVHVLEVSLSRYHNGSDPKGRVSVVRERGHKVRVVSAMETHELVLGHAARRRLFKGLRRERRLRDTLKGDFEATTKAFVGCAG------TVISSDMKSASDLIPLSVASAIVDGLEASGRLLPVEIAGLRACTGPQHLVYPD---------GSEITTRRGILMGLPTTWAILNLMHLWCWDSADRQYRLEGHPFRATVRSDCRVCGDDLIGVGPDSLLRSYDRNLGLVGMILSPGKHFRSNRRGVFLERLLEFQTRKTVYEHAVIYRKVGHRRVPVDRSHIPVVTRVT------------------VLNTIPLKGLVRASVLGRDDPPVWWAAAVAESSLLSDYPRKKIFAAARTLRPGLSRQFRRLG-IPPFLPR---ELGGAGLVGPSDRVDAPAFHRKAISSLVWGSDAT-----AAYSFIRMWQGFEGHPWKTAASQETDTWFADYKVTRPGKMYPDRYGFLDGESLRTKSTMLNSAVYETFLGP
		ScNV_23S_Saccharomyces_cerevisiae_narnavirus_23S_RNA       TGRKFPSFSVTDRPARARLAKVYRMGRRLLVGVVCRGESVVSDLKQECADLRRVIFEGSTRIPSSSLWGLVGVLGWTSPERAMQLTFIGRALPYGSP-----------------------DVERRALASHAATLSIPAECHPNYLVAAEQFAKSWADDNLPRKFRIYPIAVQESSCMEYSRAQGGLLQSFRKGFVGYDPAAPSADPDDLELAKERGFSRIRASWYSTFRY-----RGELKSTNQSLEARVAVVPERGFKARIVTTHSASRVTFGHQFRRYLLQGIRRHPALVDVIGGDHRRAVETMDGDFGLLRPDGRLLSADLTSASDRIPHDLVKAILRGIFSD----PDRRPPGTSLADVFDLVLGPYHLHYPDGSE--VTVRQGILMGLPTTWPLLCLIHLFWVELSDWAPARPNHSRGFVLGESFRICGDDLIAWWRPERIALYNQIAVDCGAQFSAGKHLES---KTWGIFTEKVFTVKPVKMKVRVRSEPSLKGYVFSRSSAFSCRMGG--------------------KGITGIRAARLYTIGAMPRWSRRIRDVYPGSLEHRTASQRYGEPVTVYRFGRWSSAIPLRWAVRAPTR---TVGNPVQSLPDWFTVGPAASSVAADSNAFG-----------AVSRVLRRMFPGLPRKLASAGIPPYLPRVFGGGGL----VKSTGLTTKIGAVASRRWMSRIGHDLYRSR
		OnuMV3a_Ld_Ophiostoma_mitovirus_3a                         VQYLKECTRIVQHFVSGHPVFVTDVMPIGLAGGLPT-IIPGTLRTLLRSKDSST-----IRGVLSTLAVYR------IMKMPCVLKLESITDPFKG-------------------------ISDTLPKSEIINGLASLG---------FEIPKGRSKHLLTLSNPIIYLLSAGPNHSISMMGIWKDIYAWYVSPLFPTLLSFIGRMNRGNVLIDLLRAEVSYWEATGV--------KPSVSPLDLKLGKLAIKEEAAGKARVFAMADSITQSVMAPLNSWVFSKLKDLPMDGTFNQQAPLNRLVQLYQDGLLH--DVEFYSYDLSSATDRLPMAFQKQIISVLFG-----SKFAKDWATLLVGRDWYL-------KDIP---YRYSVGQPMGALSSWAMLALSHHVIVQIAAMRVG-KLPFT------NYALLGDDIVIADKAVATSYHMIMTQILGVEINLSKSLVS--NNSFEFAKRLVTMDGEVSAVGAKNLLVALKSRWGISSVILDLYNKG---------------LALSEQDLRQRF-SSIPTVSKQFG-VDKLLWLVLGPFGFIPSKDGLSAFMKLNRSLSLVDMHILLSCVDEAKF---DLDKKTWEANIQETVHTLLRFGMLSEPAGFEVFS------DFTSSPLYSFIRGQFGNKLSALVQDKPVRRLIFDGP----LLHFNFYTEGWCDGLMEHLTKKIQSDSQET
		CpMV1_NB63_Cowpea_mosaic_virus                             FKYLKEVMRLSVRRIANIELEPSKKIFVKLNKFRFPNIIPLPICDQIIRDQNDQVLWASKRLIICLLTILSVHR---VLPTKVVPDYSTIVDPFTG-------------------------VSKTIDQKLLRKAIHLLN------------IKRVKQLKLKITGSMKAGPNGKISLLTSSVDALSFITQPTKIFTYLDFSVRVYKFRGLLLWMWMMCILLITLPYAIV--------SFMLGALIPIMGKLSVVYDQAGKARIVAITNSWIQTAFYSLHLHVFKLLKNIDQDGTFDQERPFKLLIKWLNEP-----TQKFYGFDLTAATDRLPIDLQVDILNIIFK-----NSPGSSWRSLLRIKYKSPQG-----------FLTYAVGQPMGAYSSFAMLALTHHVIVQVAALNSGFTTRFT------DYCILGDDIVIAHDTVASEYLKLME-TLGLSISSGKSVIS--SEFTEFAKKLKGRNNFDIFYRSWFSIIHFEKQILHLCTVFELLRRG-------------------VCELYDLYPQYINKLPKIYLRYNLLIDWVVVAFTNQILIGDRPRADGIRLFDYFVGLEVIPPLLRIMLH---TIKKDWNGLWNSIKYTLNKGFVVSQVR--------------VGLPDWTELFLLPILPSTYIIIRDYCRSFNDLTKL----FGEWWLLR----FESESYQVSILDVIDRLA
		Qbeta_Enterobacteriophage_Qbeta                            PKFGISPDQFRNSYLRAEIMSKYDSFSLGINTEAVAWEKFLAAEAECAKTNLRLYR----------------------------PNYNEDFNFSLG------------------------ETCIHMARRKIVKLLGDSVP---------------------FEAVLRHCRFSGGATTTNSRLYGHPSFKFALA----------------QECTPRAVPYVQALKACTN--------MDLGITKVSPFNKAVTVPKNSKTDRCIAIEPGWNMFFQLGIGGVIREKLHLWNIDLNDQTINQVRAYSGSCSN--------ELATVDLSSASDTISLALVELLLP---------PAWFKVLTDLRSRRGMLPDG-------------RIITYEKISSMGNGFTFELESLIFAALARSLCELLNLQPS-----SVTVYGDDIILPSD-ACSSLIEVFS-YVGFRTNEKKTFFDG--PFRESCGKHYFMGVDVTPFYIRHRIVSPSDLILVLNQMYRWATID--------------------GVWDPRVYPVYTKYRRLLPDILRRNVVPDGYGDGALVGSVLTSPFAENRGWVRRVPMIIDKKKDRVRD---ERGSYLYELWSLQQLECDSEFP----------------------------FNGSLVVGTNDGVCTYRHRERVSTAI----SDSVGAYDIVWIPCSSR----VLAPYGDFR
		CeMV_Celery_mosaic_virus                                   IKYMKSVRLHITRYICRKPLFIND-SGVSVDKSGFP-TKFIELKKFLNNHESSICYHTRLRIILTLLLLPRGLKPTKIEDAKIKPNFSSITLPFSGT------------------------RMNPIPTWFIKEFVKEYN---------LKLEKP------TYDLSKHYLSPKGGPMGKSTWSSIWSMYALKHE--LHLSLSYFLG----EAYKTLFYLPYLKNMALSY--------GHDVPPKQWPSGKLGIVKDPEGKRRIIAMVDYHSQLVLRSIHDGLLNKLRNLPQDRTYNQD-PNNAW-EENKE--------CFHSLDLSSATDRFPVKLQSRLLTEMYSD----PSFGENWMNLLLNRDYLLPE-----EGLSGERLRYAVGQPMGAYSSWAAFTLSHHLVVAWCTYKSKKVIRSS------QYIILGDDIVIKDNDIARKYIGQMS-KLGVAISMQKTHVS--KDTYEFAKRWMHKGVEISGLPLKGIFYNISHMRRMYTIIFDYLQR--IPSKSNLTSLQLFASCLSGIKFGKRV-YSKALILKLLRNFNISLRYSYGLLTPYELREYILTGFNMGDEVLPSDNRILEWFKGIICD---GVAGKVSTLSREYTKEVNSLEEHRSSQHILNSINIEITYENLQWSPLIIGMFNHINKVSEKCG-EWLYGDVPLMDI----IQQFTLPSADSLSRKDRDINKKIDELDSLI
		L_dsRNA_Sclerotinia_homoeocarpa_mitovirus                  VQYLKECTRIVQHFVSGHPVFVTDVMPIGLAGGLPT-IIPGTLRTLLRSKDPST-----IRGVLSTLAVYR------IMKMPCKLKLESITDPFKG-------------------------ISDTLPKHEVINGLAALG---------LETPKGKSKHRLTLTNPIIYLLSAGPNHSISMMGIWKDIYAWYISPLFPTLLSFIGRMNRGNVLIDLLRSEVSHWEATGV--------KPSVSPLELKLGKLAIKEEAAGKARVFAMADSITQSVMAPLNSWVFSKLKGLPMDGTFNQQAPLNRLVQLYKEGLLH--DVEFYSYDLSSATDRLPMAFQKQIISVLFG-----SDFADDWATLLVGRDWYL-------KDIP---YRYSVGQPMGALSSWAMLALSHHVIVQIAAMRVG-KLSFT------NYALLGDDIVIADKAVATSYHMIMTQILGVEINLSKSLVS--SNSFELAKRLVTMDGEVSAVGAKNLLVALKSRWGISSVILDLYNKG---------------LALSEQDLRQRF-SSIPTVSKQFG-VDKLLWLVLGPFGFIPSKDGLSAFMKLNRSLSLVDMHILLSCVDEAKF---DLDKKTWEANIQETVHTLLRFGMLSEPAGFEVFS------DFTSSPLYSFIRGQFDNKLSTLVQDKPVRRLIFDGP----PLHFTFYTENWCDGLMEHLTKKIQSDSQET
		GaMV_S1_Galinsoga_mosaic_virus                             VKIFKQIRLHVTRYLCGSPLRINS-MMIGIDKDGWP-KMINFLKPLANGTRSDK------QLLLSILFITRSFVEK--DKSKLVPDWSTITQPRTTQ------------------------KEYIIPSGFIKDWVLNNH---------LGTYKS------EFDDSNHFVSVKSSPTGPSTLTALWGLWNHSYE--SFNWLFKITSLSGVDYLTKIMNWTWLKDLGNKK--------NNKWSKQFLG--SLSLIYDPECKVRIVAMLDYTTQLFLRPIHNDLFKLLKKLPQDRTFTQN-PLNDW-EDNEH--------SFWSIDLTAATDRFPISLQRRLLLYIYSD----PEIANSWQNLLVHREYAR-------NGLN--PIKYSVGQPMGAYSSWPAFTLSHHLVVHWCAHLCN-INKFK------DYIILGDDIVIHNDNIAKKYIEIMG-KLGVGLSNSKTHVS--KDTYEFAKRWIHKGQEISPLPITGIVNNITNPYIVLMNLYDFFKIKRNQYNFSGDILTMLLKLYQGLKIYKGD-KSKKHYYLSLNRFKNLDIFLFALNNTFGYSTYDHKRSFLISKDYSKDLPGPKIMQDLISY---VISTGLSNLTVESVNKSLKFVDTIIDNKNLLNIE---DPNDLSNLPLFKGFQAYISNLRKTVE-GWNNKSISLIEA----SRGLVQMDILPIMKGSNRKILELQTIGKIY
		RsM2_1A1_Rhizoctonia_solani_virus                          IKWLKGCSVAIQKCLGKDILKSLRVLTPDLPLNGLS-RGLPRIIPVEDRVKIRRGHVPTIRFWLGLFNLYR------VLKAPSELKLGTITNKFTGDRDGLRALMRFALKFNPFVEFNKLDKKSLAPTKFIMSRSASPSNKVSWFGILTDTRLLREGSPRLWENIQAYLTMVGADQFRFDLDYACSLADRLKSFDDKVDSQGQWIRQVSKSGQVLTQVDSMKSKDSIR--------GHGIGP-GLGLSQFALKEEAAGKIRLFALMDSITQSVMSPLHDYMFAILRNIPNDGTFDQEASIARSQEKAVTAG------KAFSYDLTAATDRLPVILTAFILSTIVGI----RTFGGLWRSILVKRPFGFNSNVAEKLKVSDGPYFYEVGQPMGALSSWPGLALTHHWIVQVAAFRVTNSKSWNT-----EYEILGDDIVIFNELIAQEYLNIMA-VIGCEINLNKSISSRCRPVFEFAKRTCWGFAIVSGISLAQIRAGWRIGGRVANALQFARAG----------LLEPGESLLQAILSRNTFSKGRVLPGYKTESVTSQKALALGVLALLGER---------FRSGIIPLRTVMHAIIDPISK---NLDLKGDAIAIPIKASLHAAYQALVE----------------GDKPQLYPFSKEWNREPKFLENEDKLASRLLHSA----LNKVIILRDQYNWFIAENASEMYFPLSYLN
	;
END;

BEGIN CODONS;
CODESET * UNTITLED = Universal: all ; 
 END;

BEGIN ASSUMPTIONS;
OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS ; 
 END;