#NEXUS
[written Mon Feb 29 16:34:19 IST 2016 by Mesquite  version 3.04 (build 725) at JEYANASIM/10.20.39.18]

BEGIN TAXA;
	TITLE Taxa;
	DIMENSIONS NTAX=37;
	TAXLABELS
		CaDof1 CaDof2 CaDof3 CaDof4 CaDof5 CaDof6 CaDof7 CaDof8 CaDof9 CaDof10 CaDof11 CaDof12 CaDof13 CaDof14 CaDof15 CaDof16 CaDof17 CaDof18 CaDof19 CaDof20 CaDof21 CaDof22 CaDof23 CaDof24 CaDof25 CaDof26 CaDof27 CaDof28 CaDof29 CaDof30 CaDof31 CaDof32 CaDof33 CaDof34 CaDof35 CaDof36 CaDof37 
	;

END;


BEGIN CHARACTERS;
	TITLE  'Matrix in file "jeya.nexus"';
	DIMENSIONS  NCHAR=555;
	FORMAT DATATYPE = Protein GAP = - MISSING = ?;
	MATRIX
	CaDof1   MNCETNNNMFVKDSSIMLFGKKIP----------------------------------VPEYHIPATSQKGCQIQANSTPMNSCSNTKHTGVEIFHTENYEKSKTSS-----------------KVNNSIPLEEKKETSNTDQEKVLKKPDKIVQCPRCNSFDTKFCYFNNYNVNQPRHFCRNCHRYWTAGGTMRSVPVGSGRRKNKHIASQYRHIIATSNGNP------IERLDIENTSRYQNVSTDKSIVLKFG-----------------------------------------------------QFGHDTSFREEEESSLCVSSISNGYTRGNELSESEYNRSNS----------LQSYPASQWMVPLNQSWNNAS---------------------------------SIAQSSMQWCH--------APMVAVKNILTPNIPLQFVHGSYWHG-------NGTVSISSNGCISPSSTSSNSCCS----AMILMKSQNVLYG--------------LY--------------------------------
	CaDof2   -------------------------------------------------------------------------------------------------------------------------MEGINDL----NSCR----MSEKKTRVE--EQLNCPRCKSSNTKFCYYNNYSLTQPRYLCKTCKRYWTQGGSLRNIPVGGSSRKNNKLISS--------------------------------------------------SSQNNIIKG-------------------------------------HDLNLAFP-SMDKYP----------------------------ASMFSSTSGLINNSATNYVPN--NSLMMMS----------------------------------SSDASG------------------------------------QEIKPTNLGFSLENRYSNSY----EVQVQE-----NVGTLLFPFGDMN--QISTTHHVEVEHDK----EQGNSTGYN---WNGVIGEGSS----W---
	CaDof3   -------------------------------------------------------------------------------------------------MFSNCEKMVAISSTTNQWPQNEIDD---------GNNKVMEKQQGEEQILIQQQGALKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKRYWTRGGTLRNVPVGGGYRRNK---RTTTTN---------TTLIKKPTTLIDATSISP-----------------MFYGLSSSNNN--------------------------------------NPRPC-DVNLIPLS-RFNLSRVSNS--GYD-----------GFSTGFMSS----ETN------GYNTSGFNS------------------------------VMPSVLSSTTLQLQHKFMN------DGLKYGSNNFQVGLD--------------EEKKVEGQNSKFEWN----NG----VCQNQIEHVGLYDDSISNSSLYWNIGSSS----GIGVWNDQGAN---IASSLTSLI---------
	CaDof4   --------------------------------------------------------------------------------------------------MGLSSKQVSSNRD-IDWNQTLLQDQN---LELPKSLPMKK---QQQQQQTQQSEAVKCPRCDSTNTKFCYYNNYNKSQPRHYCRACKRHWTKGGTLRNVPVGGG-RKNKRLKKSTPPT----------SINTSTNTTINTTTKTS-------------------ISTTPTTSN-------------------------------------TNMDADFNTNMTKIQT----SHQKQN------------------------------LSEFGIGNGMFLSTSMP-------------------------------FTQNQSFLFPFSNSTSFDTNTCAAVSTSLKSSNNVYNYG-------------EEFKTMEDSN----INSVIPSTSGGNITQPWEMP---ATSNGMEMSNYWSWEDIDS-----LVSTDLNVP---WDDSDIKP----------
	CaDof5   -MSETE-----KDPVFKLFGWKIP----------------------------------LPE----------CQIPANSPPKDTCSSTKKTEVEILSSEKNEQQENSSDSMDSKQESQHNMKEKEPKENSKPAEDDRETSETDEDKTLKKPEKIIQCPRCNSLDTKFCYFNNYNVNQPRHFCKNCQRYWTAGGTMRNVPIGAGRRKNKHLVSQYRHIIVTSDGIPNTSSSGHNHVSSLDLSGCYRSSSDNETVLKFGPDTP-ICEPMESMLNLQQQKRSA------------------------------DADSISTVQHREEPSLCRSSVTNTGTQGNELSEQ--NMSNW----------FQCYPVHPWVLPMNPSWNNVASMAAVHP-----------------ISASMCNPYSAAPTAMQWCP--------APLLAIPGIRPQNIPLQLVSASHWNGQPILAAGTGTVSIGSSACISPPSSTSNSCYSGNGSATLGKHTRDTVFADEDKSDKHVQVRKMLRIDVTDEDPKS--PIRATLAIKKPNEQGKESI-
	CaDof6   -------------------------------------------------------------------------------------------MIQELFGERNYSSINGGGGGGGVLLQPLTQSPSNSQAPSSTTTITTTVTSTTTTTTSSENQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKNIGVSNTAAKT-----------SANKM--------------------------KMVASEFIGRSVHGQGF--------------------------------DLEHMVPPTSQIL-------WGSPQNSHLLSLLRSNQTQNPNPNHVTTKE----EENINLMGSSSSHSHMMTSEPLISN------------------------MLVNQRTTGGLVNSYDGVGHVLCNPFWRNNQNGNFVLGEQQHQHHHQNSEIHQLYQKLRSSTSSSSGNNNNNNYCSEISGAPVFLGNVATNSSSISNILETTFSVGGG-GELGYWNPTLS-----WSDLQTTNGSTPYP----
	CaDof7   -----------------------------------------------------------------------------------------------------------------------------MPSSDSADSRRSTKPQTRPGAPAPEQENLPCPRCDSTNTKFCYYNNYNYSQPRHFCKACRRYWTHGGTLRDIPVGGGTRKNAKRSRTHHVAVT-----------SSSST--------------------------VTSAPEHH-------------------------------------------FHSMAPISAAQ-------GGS----------------LPFGGGIDGDG----KQNMSVCG---SFTSLLNNNVQNSG------------------------FLA----LGGFGLGLEEMGFGIGRAGWG-------------------------------------------------------FPGMVEGSNMGVSSGIGNTWQLEGGEGGFVGAADCFS-----WPGLAISTQGNGFK----
	CaDof8   -------------------------------------------------------------------------------------------MQEIHSIGGG------------------TKFFAAGTADRRLRPHNNNH---------HNHQALKCPRCDSINTKFCYYNNYNLSQPRHFCKNCRRYWTKGGVLRNVPVGGGCRKSKRSNKPKNSS-------------SSSET--------------------------TALPGTPPETE------------------------------------NKSNSHSSSESSSLTAAAVTEAVSTPSATNTNSKKTQESKLLSHVNQSNTDLGNDSLEQGTGDCGIFSEIANFTSLITS-----------------------------SNEALPFE----FGN--GNGNDFQWQ-------HQKVMTVTGNQPNH-NEDVLKLLPGNM-------GAGASLMDGVDFSALQNKTSNGGFGPLDWHGDGGADHGLFDLPNTVDQGYWAHTHWSDQ-DHSNLFHLP----
	CaDof9   -------------------------------------------------------------------------------------------------------------------MDTSQWAQGIGVVKQMENPCSKEAPMLERRARPQKDQALNCPRCNSTNTKFCYYNNYSLSQPRYFCKTCRRYWTEGGSLRNVPVGGGSRKNKRSTPSSPSP-------------SSSQIPSSTITKNIILNNHDLASQNNNTNFPHSASQNPKIHQG------------------------------------QDLNLAYPPPQEDYNTLSKFIE--------------LPYEQDKPNTTTTTNNNNNNNSSSSPSSHLSAMELLKTG-----------------------------IVNSSSSSRGLNSTNFMMPMSISESSAAAAAMYNSTGFAN----LQDFKPG-LNFSVVEGFENGYGGLEGIEESG-----SGARMLFPVEEMKQQVPSSDHEFDEQNNIN-TRNQGDSSGF----WNGMLGGGS-----W---
	CaDof10  -------MLEARDPAIKLFGKTIPVSEISPGSGDSTGAPASSSSGDAVD----DVICQNHVSS-NTEMDGEEREIDEESKEEEVIECNKEDKTITQSSEKIA--DLDTSSRGEESIKPSNEEEESTLKTAKNKEEQSE--NSQDKTLKKPDKILPCPRCNSMETKFCYYNNYNVNQPRHFCKNCQRYWTAGGAMRNVPVGAGRRKNKN-FASHYRQITIPDVIVQNSQSDSPNGVHHHS------VNCNGTAFTFGTDTP-LCESMESVLNIVDKAVTSCPTN-GFNRPEELRISVPYAGEEKSNDHSNKSSDASTTPTEDATTNSSLEQVVQNSQSFAPQFPHY-PSAPWVLPWSPSQWSSQVQSPHAFFPQGIAMPLYPPPAYWGF-----------------TMPGAWNNPWLAQPSSPS--------SATPSSPTLGKHSREENTLTSNDAVGSDEQSSKGNNKEKSLWVPKTLRIDDLGEAQKSS----ILTTLGIKNSKPDSICGGGLFKAFQPKGDEK-EDTQNSP--VLQANPAALSRSISFHETS-
	CaDof11  --------------------------------------------------------------------------------------------------------------------------------------------MLERKARPQKEEAINCPRCNSINTKFCYYNNYSLTQPRYFCKTCKRYWTQGGSLRNIPVGGGSRKNKTTTTSNSSK-------------NLPQT--------------------------LLSQQNHKIHHEEQK---------------------------------QDLNLRSCGNITDLIQQN--------------------NNKSSVSSSTSTTTIDPISAASTSHHNLSALELLTG---------------------------------ITTSSRGLQYS----FMPLVQGDNSNNVYSNNCGFP-----VQDFKQVPMNFSLDGIGGSEFASVDHHHHHHGVEESSEGRVLFPFEDLK--QVSSTSLTLDQNNIK-DQQGYNSSGF----WTGMLGGGGGGGGSW---
	CaDof12  -------MQETRDSTISLFGHKIPLS---------------AGDRDGG--------EGYEGEQELHEEKYQTHE---DPEAENVTERVQETYPPSNLEEAEN--SGNSSPEGITNLKTPSIEEEIAKSKDDKSEKE----QSQEKTLKKPDKLLPCPRCNSMDTKFCYYNNYNVNQPRYFCRACQRYWTAGGATRNVPVGAGRRKNKN-SASHYNHITISEA-LQEATIDSPNGTHIHS------LKSNGRVISFGSDAP-ICDSMASVQNTGEKKVVDGTRN-RFHGLE----DQSLHGEN--GDEYSSVSNSMGESNKSTTSTFPQPVLQ--NNGFLPQLPCM-PNVPWPYTWN-----SPVPPPHGLCPLGFSFPIYQP-TFW-------------------NVPWFPSHSYASSSMSPS---------SGPNSPTLGKHSRDSEQDS--------SHKEPSKHRNGRVLVPKTLRIDDPSEAAKSS----IWTTLGIKN---ESASRGGMFKAFQSKR-GERNGIETSS--VLMANPAALSRSLNFHENF-
	CaDof13  --------MGEENQGIKLFGAIIK------------------------------------------------------LHDEELKEGEKGSEDLTVE--------------------------------------------------KKPEEIIPCPRCKSMETKFCYFNNYNVNQPRHFCKTCQRYWTSGGALRNVPIGAGRRKPK--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PTDGALYETN----------------SGDGHDKFGLVLDKWQVDTAESN-------------------------------FRQVLSGKRRRTTSGG-----YSLALL-----------
	CaDof14  --------------------------------------------------------------------------------------------------------------------------MSSNSSLENMLGCSKE-EQD-TKAKPQPEQALKCPRCDSTNTKFCYYNNYSLTQPRYFCKSCRRYWTKGGTLRNVPVGGGCRKNKRSS--STSK-------------RVQDQSFTPNLIN-------------------PFNNFPHSSYDHNS---------------------------------NDFTLALARLQKQSCGQMGHFD-------------DNDVSILGNPNSA-TSSFNDVIGNH----STTNNGLF-----------------------------------DAIRSGLFLGSGIQYNYNNNNVQNLYGVYGNGDNMEVNSGNNNSNVCGVGEEMMFPYEQEIRGAINVKQELCSGREQSESK---VFGGFPWQLN-GGPNMGEIESVR-GNWNNGFTSN----WQGVLHSPLM--------
	CaDof15  -------------------------------------------------------------------------------------------------------------MPSNNFKNTPSTKQDHENQQGSCSSLDSKKPPTRPSSSQNQQGVIKCPRCDSPNTKFCYYNNYSLTQPRHFCKTCRRYWTNGGALRNVPIGGGCRKKQKLKTSS--RFS-----------SCNES---------------------------INKFSPSLDFHLGNLP--------------------------------LPLLPFSPKLHLHNFQPSFYNNNQFSSNSNTTTSSTFQLDPSSTSSNSLMGLNLYPFSSTIGSGLFNGANENPIQQGMN----------------LMNVNSTSTTSNSTSLATSIESLSSMNQDLHLKLQQQRLATMFGGGDNDNKKEQSSNVLTQPILFQNLDVSKTEMFGDLRKDQGSS--GDVPMEWFFGNSYSSMITPTTTINGGNDNGNNNWSNGVNV-----WGDVQQQQPYTALP----
	CaDof16  ------------------------------------------------------------------------------------------------------------------------MLHLLSSSSSSPIPLSTSMDKSNSRWKPNIEIAPNCPRCASTNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCRKTRRGKTIRNSH---------------------------------------------------------------------------------------------TDRLSANGSEDDADGHHHQSQNNGSRDIDMALVFAKFLNQNPTNSDHGEEFENENEPINNGSPSSNNINNLSTPESVET--------------------------------------------ENDAVVHPQNPFDADSVALNGELSLSGIDEFEGFLGVDEDVVQDVLWSHSDANANVNAMMMVSSSNYTWQQPSSMMQMDELEYSMPLPILNENVGILGVPLIFQLWKSSHQVQDLNYY-----
	CaDof17  -------------------------------------------------------------------------MVYTSLP-PYMDPANWHQQQPNHQVANN--SFNTPLLIP-SPQPQPSNLTPSQSHGGSIRPGSMAD-RARMANIPMQEPAQKCPRCDSTNTKFCYFNNYSLSQPRHFCKTCRRYWTRGGALRSVPVGGGCRRN-KRTKSSNN--------------NTSKS--------------------------PVSSDRQTSSA--------------------------------------NNNSP-AVLSSQTP--PPMRFMAPLHQ----LGDHIG-EIG-LNYGFSS------PMGGVGDLNFHIGNSLGGASGGVG---------------------------SGGVTSASGGSASILPVGGFEQWRMP-----QTHQFP-FLSGLEASS-SHGLLYPFEGGGGGGNDQAHVYGGVPKVLSTSSVKMEENQSRQFLGMINSNNNNPNSEQYWNASAGGATSAWADLSAFNSSNSTTTNSNYRS
	CaDof18  -------MTEIKDSAIKLFGRTISLPLN----------PNDSS--------------SPSSPTQLNSAIQHEPE---EPSRKELTTVQDDDASQQTTEDLKSP--TTSSAILENPPKTPSAETESSLPKSSTNGEQSETSVSEEKTLKKPDKVVPCPRCNSMETKFCYFNNYNVNQPRHFCKNCQRYWTAGGTMRNVPVGAGRRKNKNPSTSHYRHLMIPEA----AKLSSPNGLHNSV------LGNGAAVLAFDSDSP-LCNTMASVLNIAERHQNRMPNV--FHHATEPNTFVSYGGEN-------DHSITTPTLSERKDHTGSNGSMDKRVDGFPPQLQYIPSTLL-PYPWNP------AIPPPTFCPPSYPLAFYTPPPYFG------------------CMPPSWNISCISPQSTSSVNHCDSLHRSIPYSPTLGKHSRDGNIITPQN----EKHDQEHSNTESSVLIPKTLRFDDPSEAAKSS----LWSKLGINNDKANSINGGTMFNAFQSKGKDKNHSVEAAASTLMYANPAALSRSRTFHEQT-
	CaDof19  --------------------------------------------------------------------------------------------------------------------------MS-NESLENMLACSKA-QQD-KKPKPQPEQALKCPRCDSSNTKFCYYNNYSLSQPRYFCKSCRRYWTKGGTLRNVPVGGGCRKNKRSSSLTSSK-------------RVQDQTFNTNIPN-------------------PLTCFPSLSYDTN-----------------------------------DLTLALARLQK---GQLGFEH-------------EHDFSKFGNHTSTNTNTSCDILNNHGLNNSSTNQGFL-----------------------------------EAL-----MGSQNNVYYDN------VGVSG---EMMLP----------YDHEMSIATTQAVS-VTTMKQEMCNVREQNENR---VLWGFPWQLN-GDTNMNEVESGR-ASWN-GLTPS----WHGLLNSPLM--------
	CaDof20  ---------------------------------------------------------------------------------------------------------------------------------------------MESTSWKSNEISPNCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRRYWTKGGSLRNVPVGGGCRKNRRGNNNNKILR------------QSFDSLTFKN----------------------SPNCDTSSDN--------------------------------------NNNISIGHCYDPMMRNITNVSSSSSSPNIDLALVYANFLNQKPNCENSNQIQTTSFDSPSLENSMLSPSKIVTHFS------------------------------------------------ESNNNHEMYCSEFNSMQSFQKDDRIDHQQQCSNIHDDDGGVNFELPPLPGEEESSAHDDVLWSNSDEIMMNLPFQVTQQPTPLLGPEIDHDADLLNIGNWCPFDFPNDASFSRP--------
	CaDof21  -------------------------------------------------------------------------------------------------------------------------MEGIAP-----NSCTRQ--VLEKKARPQ--EQINCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGGSLRNVPVGGGSRKNKKITPNPSKI-------------PDLNPPT-----------------------LQVSSQNPKMQGG------------------------------------QDLNLSFP-SMENYHHH---------------------HHHHGMSSFVHHEMHNNNESSSSAPNSLSALDLLR----------------------------------SSMASRGLNPYANNNNNNNNNNNNNNSLMPNSNALYPNGFPMQEVKPS-LGFSIDGIGNRSYD---HVQEGG-----GNGRLLFPFGDVNNKQLSTS-DVEVEHNK----EQGNSAGY----WSGMIGEGS-----W---
	CaDof22  -------------------------------------------------------------------------MVFSSIP-SYLDPLNWHQQPNPHQANGSDSHQSHNLLP-----HGGGSMIRPSSIANSNQAQVQTQTQAQQPKIQPQETTLKCPRCESTNTKFCYYNNYNLSQPRHFCKTCRRYWTRGGALRNVPVGGGCRRS-KKTKKSTTT-------------NTTSS--------------------------KTPLLSNSNEK--------------------------------------DYSLSNSTSLGEF--LHPTNNRTYLTP----LG------VG--NIG-----------------------QMGFQIGDYS---------------------------SNIAVGEG--------GGGLDQWR--------FQQFP-FLNGFESNS---NVSYPFQSE-------------IVEPPTTSRVTH--MPSSVKLENINGGLNLLRSSLSISENNN-HYNSWPDFSSLASSSASHL------
	CaDof23  -------MSETKDPAIKLFGKTIPVPDILVG------TPALSS-GDVVD----ESIDQNHDSSINSSKDEQEQEIVMDTLGDKPTDGKKEDGVPTKSSEEFS--TPDAASRTGE----ESEREAATLKTSKIEEEQDETSNSHDKNLKKPDKILPCPRCSSMDTKFCYYNNYNVNQPRHFCKNCQRYWTAGGTMRNVPVGAGRRKNKN-SSSHYRQITVTESTLQNSRTDFPRRSYQPS------LKCNGTLLTFGSETP-LCESVASVLKLADRTVQNYARN-GFDKPEELRICVPHATGEKGDDQSNKSSITSTKSMEGGRTNVSQEQAMSNGQSFPLQGHYFRPGTPWPFPWNPMQWSSPVP-PPSLCQPGFSLPLYPATTYWGC-----------------TVPGAWNIPWQAQPLSPNGA----NLNSSPNSPTLGKHSREDNSIRSSDSSGTDGDGKKESSEEKCLWFPKTLRIDDSREAEKSS----FWTTLGIKNDNTNSVPSRGLFEAFPSKCDDKNHSVQASL--VLQANPAALSRSLNFQETS-
	CaDof24  -------------------------------------------------------------------------MVFTSIPTAYLDAANWQQQQQNHQQHGNGGSVSQQLLQS-PPPPQPPSQ-PNGGSAGSIRPGSMSD-RARMANMPMPETALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTRGGALRNVPVGGGFRRN-KRSKGSNAG-------------NSTKS--------------------------PASSDRQTGSASSTNSI------------------------------NSNNNHPSNDILGLTPHMASLRFMAPLHHNINNLNDFGGGDIG-LNYGFS-------YMGGGGGG----GGDLGSALGG------------------------------GNVVN------SILSSSGLEQWRMPLQMTQQQHQFPNFLAGLEGSS-NG--LYPFEG-----NTQNHH------------------------ELITSGYLRPKIVMYV-------------------------------
	CaDof25  -------------------------------------------------------------------------MVFSSIP-GYIDPPNWHQQQN-HHLQGNGSDNNTQLLPPLPPQVGGSTGVGGGNIIGSIRPNSMAD-RARLAKLPPPEPALKCPRCDSTNTKFCYFNNYSLTQPRHFCKTCRRYWTRGGALRNVPVGGGCRRNNKKNKRSRSK-------------SPSTA--------------------------TNSEKLQTTSA--------------------------------------NIPSSHHEIIGQLP-PHQITNLPFMAS----LQNLSRYTVGNMNLGNLQ------QQQE--------TDHMGFQIGSVS------------------------------AGNNN--------IGVEQQWRN-------LQQFP-FLNTFESSNSAGNNSYPFQGES---NIEASASVFVGDTGSNSRVNNNTQQPPVKME-ENGGLNLSRTSLGITEHNQ-QYFSWNDLS--GSSTNHHLL-----
	CaDof26  --------------------------------------------------------------------------------------------------------------------------------MQDP------TTFQPMKPHFPEQEQLKCPRCESNNTKFCYYNNYNLSQPRHFCKNCKRYWTKGGALRNIPVGGGTRKATKRSSTSKRSTS-----------SSSSS--------------------------PSPSIVTSSAQ-------------------------------------------------------------------ASVSESD----PTQIHVNPVE-IGGGSFSSLLS----STERFGNLFEGLN----------------------------------------SNGSGLKMVQMGEFG-------------ENLNCD--------------------------------PVVNSGHNPNSTLG---ESDTFLGLQNGDSSCWNGN-----HGWSDLAIYTPSSSYQ----
	CaDof27  ---------------MKLFGRTISLTCNTDV------STNDSSSFPREDFSHHSPYSSSSSPLEMNSSTEHQTKRHKEPSRKELTS--DDEASQQTTEDSKS---HTSSCLIENP-RTPSSETETSQ----QNGEKSD--MSQDKSLTKPDKIQPCPRCSSNDTKFCYYNNYNVKQPRHFCKNCQRYWTAGGIMRNMPVGAGRRKNK---ISHF---------------SSADSNYRQV------IPQSTAVLTFGSDS-----NMS------------------------------------------------STLHEEK--------VNKCYQNFPPQFPFQN------HPWNPS-----MIPHAAFYQQSYPVSFYPNIAYYGG-----------------FLPQSWSVQSISTQS------CE------PNSPTSGKHSRDGEILFHSNSK-KEKLGSESNNNSNSVLIPKTLRIDEPDEAAKSSS---TWSKLGIK--------------AFASKGGDKNHVVETSS--ILQANPAALSRSLVFHERI-
	CaDof28  MTEFMWLMNFIEGQIVETYPNSNP----------------------------------DLNNDWLDLTYFSTELQITRNGLEESINADVGVPLNEVSSKQENPQEDATNPIPTMNKTGTSKLAGKAVHRTNEHKTPKGDIDNQEKVFKKPDKVLPCPRCNSSETKFCYFNNYNVNQPRHFCKNCQRYWTAGGTIRNVPVGAGKRRGKHSPLQHCQVSVTPDAVPVVIHTDLNPATDKHISSSIVPSVN---IPSLGEEVP-LCESLETVLNLKSHRKIE------------------------------MDSSTVKEDIDEDPSVIAAEFGEKEYSENGIEHVGLIQQCNGLLPLHS---LHYYTAPSWTCQWNPCWNAMSTSSYWG-------------------CMPNWAGRQIEEYSFNGIP--------SPSSSASSGTFSGNRSPTLGKHCRDGSTLTEDDTMKKNIWVPKTIRINDPEEAAKSSIWSTLTTKSQQNKPVMKG----SVFKSFEPKSNAKSRNLDDNQ--ILRANPAAFCRSGSFQESM-
	CaDof29  -------------------------------------------------------------------------------------------MQEIHSIGG-------------------RNLFGD-DRDRRMR-TNYHH---------QNHHALKCPRCDSFNTKFCYYNNYNLSQPRYFCKNCRRYWTKGGVLRNVPIGGGSRKSKPSN-SNNSS-------------SSTTP--------------------------PATTRKSPPPE------------------------------------DNSNSHSSSESSTFTTPTATAEAKTPISNAT-------SKVFS-VNSAS------KPEQ----------VGSFTSLVPSTL---------------------------TNDAFSFG----FGNNVLDASSFRFG-------DSHQRGDDQVHVAQ-GGDSLGICQWQQ-------QSSYQRTSLLDHQQLAN-----GFGPLDWQG--GAGNCLFDVRDVVDQSYWTHPHWSHHVNPSSLFHLP----
	CaDof30  ---------------------------------------------------------------------------------------------------------------------------------------MADRARMSKIHQNEVAAAQKCPRCESTNTKFCYYNNYNLSQPRHFCKTCRRYWTRGGTLRNVPVGGGCRRNKRSKVNSISKS------------STSKPNHDHRSVG--------------------TGVVAGVGGS-------------------------------------SSTGANASSNNGCIDSNVNVGMAHFQTQFPFLSSLNHFNNNDYVSGGIGSLMAKNISNSTTTSVEFQLGNGSSLGNSNVG------------------------SLFLSNGIGEQWRFSNPEQVHHHPHQQQQQQQRNQQFPFLTNLEPQIGLFQFGSGENNEPPTSFIHSKAIDSSSVGIGTIPQVNNIKMEENNHQVLSLPKNLLSGSGNSNDIFWNGNGNSNANAWNNEVPSFTPSPSQLL--
	CaDof31  -------------------------------------------------------------------------------------------------------------MSPDETQPSKSAK-DKDNQNGSLGRKTS--SSSTSSSTRPQEQNMNCPRCYSPNTKFCYYNNYSLTQPRYFCKTCRRYWTKGGALRNVPIGGGCRKNKKMKSSSSSRLSC------DLKDSASSSSLELGGLN------------------FLHTISPSIDFHLGNN------------------------------------LPFPPRLQLHQNHHTPMLFNQFSSSYDETNSSTPLTTVSST-------FNLDSTQNSVAAMNYPFSNYNGVIQGMS----------------SMNIH------------TNLESLSSMNQDLHWKLQQQRLTMMFG---AENQKDNNQTQKPQPILFENVEVSKGNGGNNLCVGNSRREVGDTPSEWFFGNSYNGSVTVTAAARPTGSNGG-AGSNNWNG-----WTDVHQQ--YNALP----
	CaDof32  --------------------------------------------------------------------------------------------------------------------------------MEQEGVDGRRGEMNKQVQIHPPQPPQKCPRCDSFNTKFCYYNNYSLSQPRYFCKSCRRYWTQGGTLRNVPVGGGCRKGKRAKNSSSTSSG-----------NSSLS--------------------------QTPVLSSAQQQTMALAL--------------------------------MTKDASFSSALPFYQGGGGVGGVGYMSSFAGFNNNNQMNLPSSTHSNPFENVGGHSNLGLLQGFNVAAAALGNSTQGQNR--------------PSQFFPMGMFTSEQQQGLNLIPPCSGSGSGVGVGALTHHENWTQSFMNNNSGNNNRVND--------------------------------PSLWSTISTTTSIGGANNSDRNLGGGSGGGASVGGSSSLAPNQWPDLSGFNPSQ-------
	CaDof33  -------MIESKDPAIKLFGQNIPFSGEAEA-------LTITGNQTASP----TIMDVEQEERDFDESTNEDEEKDKEHEAEKDTEKKKETDPPPNNAETKNNNSATTLAKDIHNTKRLSIDEETSISENDQTDAATTNHNSQEKILKKPDKILSCPRCNSIDTKFCYYNNYNVNQPRYFCKACQRYWTAGGTMRNVPVGAGRRKNKNNSSSHYRHITISEA-LQAARVVAPNGTHHLSN-----LKTNGRILSFGLDHPQICDSLENVFNPAEKKGLNSTRNSEFHSIEGTKIPVSRSQND--GHNSSASSKTVANSIEESGKTMSQESLPQKNNGFIPQVPCI-TSVPWPYPWS-----STIPSPPALCPPGFPMSFYPA-AFW-------------------NVPWFPSHPSVTNPMSLN---------SSLNSPTLGKHLRNDDNDDNLAKQDHLQNEESPKQRNGSVLVPKTLRIDDPSEAAKSS----IWATLGITN---ECVSGGGMTKAFQSKKDGKKHVAETSP--MLRANPAALARSLNFHESS-
	CaDof34  ---------------------------------------------------------------------------------------------MGLSSLHACMESSAEHWLQGTIHEESAGMDSSSPISGDMLTCSRP-MMDQRRLRPPHDQSLKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRRYWTKGGTLRNIPVGGGCRKNKKVSSKKSND-------------HNHHLANNNNNIHN----------------QPQQQQMPNSYIHHNP---------------------------------KDLQLSFPDVQFSHLSNLLGTNGALGNPNFMENKYGNNVGMLEINHPRPIDFMESKLEGIIGSSSSRNFDFFGNS-----------------------------HDHMSMSMNMNMGVGVGVGGDNNMMNGQNGLPHDFHHAFGGMSFDHGNNNNIGAYNLMDSCQRLMLPYDANDEDDHNNESIDVKPNPKLLSLEWNQDQGCSDAGKESYGY-GSWT-GMMNG----YGSSTTNPLV--------
	CaDof35  --------------------------------------------------------------------------------------------------MGLSSKQVSSSGL-DNWKQNLLESQD---LELPKPHHMMRKHHQQQQQQQQTEQVLKCPRCESTNTKFCYYNNYNKSQPRHFCRACKRHWTKGGTLRNVPVGGG-RKNKRVKKSNTP--------------ITSSTTKTTTTATN-------------------AICTPSISN-------------------------------------MNGNG-LNSNMT-IQTPLGISDQKSNNIPSSLYQALIHPPSLFLQQSLMNTRDLLESKDFGIGNGIFTSTSCSTY---------------------------PILPQNQSLLFPFSTSSSFDTTTCP--------SSNVYYYG-------------EEFKTMEEPT----INSIVPST------KPWEMSLPGTTTAGMETSKYWNWEDIDS-----LVSTDLKDP---WDDSDIKP----------
	CaDof36  -------------------------------------------------------------------------------------------------MFGNCDEKTVTP---NRWTQSEIDDHHKVSMASNGSTRVMEKP-GQD-LVQQQQQALRCPRCDSSNTKFCYYNNYSLSQPRHFCKACKRYWTRGGTLRNVPVGGGCRKNKRVKRSSTTHSSNNIDNSTNTIVASPSSSSNPTSANSNPPSQ-----------LHNFDISNSTSNHINTLLYG----------------------------GGNGNSCHDVMNFPFSTRFNSRVVSSSSSGYDNLQVNNSCLGLGFSSGLLMSGSGGEVNHHYHDAGYNRNGFSSNNNNNHTLVSSYNSIFGSSSTSTNSLASTPVMTSLLSST--LLQQKFMSSTGTSSGGMKDDIFHHEMKMEGNSSSEVAGIMASKEVKLCEGQNRLQEWNNVNANGGVAVAFQNQMEHLGLSDT----SSLYWNNHNSSNTATGLGVWSDQPNN---IGPSVTSLI---------
	CaDof37  -----------------------------------------------------------------------------------------------------------------------------MPSSDSGDSRRSTKPQNRPGAPVPEQENLPCPRCDSTNTKFCYYNNYNYSQPRHFCKACRRYWTQGGTLRDIPVGGGNRKNAKRSRTHHVAVT-----------SSSS---------------------------VTSAPEHH-------------------------------------------FQSMAPISAAQ-------GGS----------------LPFGGGIDGEG----KQNVSGCG---SFTSLLNNNVQNSG------------------------FLA----LGGFGLG--EMGFGIGRAGWG-------------------------------------------------------FPGMVDGSNMGVSSGIGNTWQLEGGEGGFVGAADCFS-----WPGLAISTPGNVLK----

;


END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED  (CHARACTERS = 'Matrix in file "jeya.nexus"')  =  unord:  1 -  555;

END;

BEGIN CODONS;
	CODESET * UNTITLED  (CHARACTERS = 'Matrix in file "jeya.nexus"')  =  universal:  1 -  555;


END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED  (CHARACTERS = 'Matrix in file "jeya.nexus"')  =  'Mk1 (est.)':  1 -  555;
END;

BEGIN TREES[!'Parameters: Tree simulator: Coalescent Trees. [seed: 1456734036676]'];
	Title Simulated_Trees;
	LINK Taxa = Taxa;
	TRANSLATE
[0] 		1 CaDof1,
[1] 		2 CaDof2,
[2] 		3 CaDof3,
[3] 		4 CaDof4,
[4] 		5 CaDof5,
[5] 		6 CaDof6,
[6] 		7 CaDof7,
[7] 		8 CaDof8,
[8] 		9 CaDof9,
[9] 		10 CaDof10,
[10] 		11 CaDof11,
[11] 		12 CaDof12,
[12] 		13 CaDof13,
[13] 		14 CaDof14,
[14] 		15 CaDof15,
[15] 		16 CaDof16,
[16] 		17 CaDof17,
[17] 		18 CaDof18,
[18] 		19 CaDof19,
[19] 		20 CaDof20,
[20] 		21 CaDof21,
[21] 		22 CaDof22,
[22] 		23 CaDof23,
[23] 		24 CaDof24,
[24] 		25 CaDof25,
[25] 		26 CaDof26,
[26] 		27 CaDof27,
[27] 		28 CaDof28,
[28] 		29 CaDof29,
[29] 		30 CaDof30,
[30] 		31 CaDof31,
[31] 		32 CaDof32,
[32] 		33 CaDof33,
[33] 		34 CaDof34,
[34] 		35 CaDof35,
[35] 		36 CaDof36,
[36] 		37 CaDof37;
	TREE Tree_#_1_simulated_by_Coalescent_Trees = ((((28:2808,((15:526,(13:61,25:61):465):164,4:690):2118):1623,(((27:274,6:274):80,((26:5,36:5):267,35:272):82):450,((12:17,(23:7,34:7):10):293,31:310):494):3627):1695,3:6126):6087,((11:1065,8:1065):2001,(((((((20:162,(19:132,(18:19,(32:5,33:5):14):113):30):24,9:186):124,24:310):97,7:407):445,((1:569,((30:188,14:188):54,29:242):327):269,10:838):14):368,((22:227,(5:9,2:9):218):746,16:973):247):307,((21:163,17:163):249,37:412):1115):1539):9147):0.0;

END;


Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		timeSaved 1456743861279;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 1597323707686726166;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 6252132628152838011;
			mqVersion 304;
			checksumv 0 3 1165019793 null  getNumChars 555 numChars 555 getNumTaxa 37 numTaxa 37   short false   bits 1048575   states 1048575   sumSquaresStatesOnly 1.1648843436542E14 sumSquares 1.1648843436542E14 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 1362 685;
			setLocation -8 0;
			setFont SanSerif;
			setFontSize 10;
			getToolPalette;
			tell It;
			endTell;
			desuppress;
		endTell;
		getEmployee  #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
		tell It;
			makeTreeWindow #1597323707686726166  #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
			tell It;
				suppressEPCResponse;
				setTreeSource  #mesquite.trees.StoredTrees.StoredTrees;
				tell It;
					setTreeBlock 1;
					toggleUseWeights off;
				endTell;
				setAssignedID 945.1456734058841.3808162867373627964;
				getTreeWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 1262 613;
					setLocation -8 0;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
						setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow;
					endTell;
					setActive;
					getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
				tell It;
					suppress;
					setTreeDrawer  #mesquite.trees.SquareLineTree.SquareLineTree;
					tell It;
						setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
						tell It;
							branchLengthsToggle off;
							toggleScale on;
							toggleBroadScale off;
							toggleCenter on;
							toggleEven on;
							setFixedTaxonDistance 0;
						endTell;
						setEdgeWidth 4;
						showEdgeLines on;
						orientUp;
					endTell;
					setBackground White;
					setBranchColor Black;
					showNodeNumbers off;
					showBranchColors on;
					labelBranchLengths off;
					centerBrLenLabels on;
					showBrLensUnspecified on;
					showBrLenLabelsOnTerminals on;
					setBrLenLabelColor 0 0 255;
					setNumBrLenDecimals 6;
					desuppress;
					getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
					tell It;
						setColor Black;
						toggleColorPartition off;
						toggleColorAssigned on;
						toggleShadePartition off;
						toggleShowFootnotes on;
						toggleNodeLabels on;
						toggleCenterNodeNames off;
						toggleShowNames on;
						namesAngle ?;
					endTell;
				endTell;
					setTreeNumber 1;
					setTree '(((((((((2:9,11:1065):702,21:163):351,9:186):351,(16:973,20:162):2747):1623,(32:5,(34:7,(14:188,19:132):1019.25):906.75):1813.5):3891,((3:6126,36:73.0625):73.0625,((22:227,30:188):1000.5,(24:310,(17:412,25:30.5):177):402):500.25):500.25):1945.5,((8:1065,29:242):305,(26:458.65625,((7:407,37:412):442,(4:802.5,35:88.5):44.25):44.25):1.90625):3.8125):972.75,(15:526,(6:68.5,31:499):68.5):445):972.75,(13:61,((12:17,33:1290):247,(((23:7,27:274):218,10:419):419,((1:1315,5:9):54,(28:1404,18:19):557.5):139.375):139.375):278.75):1.0686E4):0.0<> <> <  setBetweenBits = selected >;';
					setDrawingSizeMode 0;
					toggleLegendFloat on;
					scale 0;
					toggleTextOnTree off;
					togglePrintName on;
					showWindow;
				endTell;
				desuppressEPCResponse;
				getEmployee #mesquite.trees.ColorBranches.ColorBranches;
				tell It;
					setColor Red;
					removeColor off;
				endTell;
				getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
				tell It;
					setAlwaysOn off;
				endTell;
				getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
				tell It;
					colorByPartition off;
				endTell;
				getEmployee #mesquite.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles;
				tell It;
					setOn on;
					setDigits 4;
					writeAsPercentage off;
					toggleCentred off;
					toggleHorizontal on;
					toggleWhiteEdges on;
					setFontSize 10;
					setOffset 0  0;
				endTell;
				getEmployee #mesquite.ornamental.DrawTreeAssocStrings.DrawTreeAssocStrings;
				tell It;
					setOn on;
					toggleCentred on;
					toggleHorizontal on;
					setFontSize 10;
					setOffset 0  0;
				endTell;
				getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues;
				tell It;
					panelOpen false;
				endTell;
			endTell;
		endTell;
		getEmployee  #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
		tell It;
			showDataWindow #6252132628152838011 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 1262 613;
					setLocation -8 0;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
					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;
					getInfoPanel;
					tell It;
						btspOpen true;
						apOpen true;
						fpOpen true;
					endTell;
					toggleInfoPanel on;
					toggleEditingNotPermitted off;
				endTell;
				showWindow;
				getWindow;
				tell It;
					forceAutosize;
				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;