#NEXUS [written Mon Mar 04 18:57:25 EST 2013 by Mesquite version 2.75 (build 566) at d-i191-19-46.student.eduroam.uq.edu.au/10.191.19.46] BEGIN TAXA; TITLE Taxa2; DIMENSIONS NTAX=35; TAXLABELS Anopheles_gambiae_tyr5 Anopheles_gambiae_tyr4 Anopheles_gambiae_tyr9 Anopheles_gambiae_tyr8 Anopheles_gambiae_tyr7 Anopheles_gambiae_tyr2 Anopheles_gambiae_tyr6 Anopheles_gambiae_tyr3 Drosophila_melanogaster_tyr3 Bombyx_mori_tyr1 Bombyx_mori_tyr2 Tribolium_castaneum_tyr2 Tribolium_castaneum_tyr3 Tribolium_castaneum_tyr1 Drosophila_melanogaster_tyr2 Drosophila_melanogaster_tyr1 Anopheles_gambiae_tyr1 Daphnia_pulex_tyr Limulus_polyphemus_HcB Euphrynichus_bacillifer_HcA Mastigoproctus_giganteus_HcA Limulus_polyphemus_HcA Euphrynichus_bacillifer_HcB Mastigoproctus_giganteus_HcB Epiperipatus_sp_Hc Dictyostelium_fasciculatum_tyr Polysphondylium_pallidum_tyr2 Ciona_intestinalis_tyr1 Saccoglossus_kowaleksii_Hc Ciona_intestinalis_tyr2 Ciona_intestinalis_tyr4 Ciona_intestinalis_tyr3 Amphimedon_queenslandica_tyr Aspergillus_nidulans_tyr2 Aspergillus_nidulans_tyr1 ; END; BEGIN CHARACTERS; TITLE 'Beta alignment_NJ'; DIMENSIONS NCHAR=365; FORMAT DATATYPE = Protein GAP = - MISSING = ?; MATRIX Anopheles_gambiae_tyr5 HRQDTQDIDLPSFIESFYVDSKDYTASDLEEEHRLAYFREDLGINLHHWHWHLVYPFEVVAKNRRGELFYYMHQQIIARYNFERLCNKLKRATRFDFNEAEAYFPKLDAWPSRVANQKLRDDVEDLKRWSDRIYAAIHQGSVDERGRSITLTIDILGNMIESSILSPNRTYGDLHNMGHVFISYIHLESFGVMGDSATAMRDPIFYRWHSYIDDIFQEYKATRYTENQLNYPGITVSNIEVQSKNTFNTFWQQSDVDLSFTHLQHQPFTYKITVNGNRKGTCRIFLAPKTRDQKIMFIELDKFTVNLKQGQNTITRASSQSSVIPFERTLAQFNFCGCGWPQHMLIPKGTPEGMKSQLFVMISND Anopheles_gambiae_tyr4 HRQDTQDIDLPSFIESFYVDSKDYTASDLEEEHRLAYFREDLGINLHHWHWHLVYPFEVVAKNRRGELFYYMHQQIIARYNFERLCNKLKRATRFDFNEAEAYFPKLDAWPSRVANQKLRDDVEDLKRWSDRIYAAIHQGSVDERGRSITLTIDILGNMIESSILSPNRTYGDLHNMGHVFISYIHLESFGVMGDSATAMRDPIFYRWHSYIDDIFQEYKATRYTENQLNYPGITVSNIEVPSKNTFNTFWQQSDVDLSFTHLQHQPFTYKITVNGNRKGTCRIFLAPKTRDQKIMFIELDKFTVNLKQGQNTITRASSQSSVIPFERTLAQFNFCGCGWPQHMLIPKGTPEGMKSQLFVMISND Anopheles_gambiae_tyr9 HRPDTQNLDLPSFIHVFYVDSQDFTASDLDEEHRVAYWREDIGLNLHHWHWHLVYPFEIVDKNRRGEIFYYMHQQIIARFNIERLCNGLKRVVKLNWREPEAYFPKLDTWPARPVNQVPRDSLDDMDRWRDRIYDAIHSGVVGDNGQNIPLTIDVLGNIIESSILSPNRNYGDFHNMGHILIGYIFLEPFGVMADPAVDLRDPLFFRWHAYIDDMFQEFKATRYTVAQLNYPGVTVTNIEVQKPNVLSTFWQQSDLDLSFTHLQNQDFTYKITVNNNRMGTCRIFLAPQFRNQKDMFIELDRFAVSLKQGTNTITRHSTESSLIPFERTLSEFNFCGCGWPQHMLLPKGTEAGYPCHLFVMISND Anopheles_gambiae_tyr8 HRPDTQGLDLPSFSQTFFIDSQDYTASDLDPEHRLWYFREDLGINLHHWHWHLVYPFEIVAKDRRGELFYYMHQQVIARYNAERFSNNLARVLPFNLRDPEGYFPKMDAWPPRFESTRLSDEIGDLERWRDRIYEAIHQGFVDERGNRVPLDIDTLGNMIESSILSPNRVYGDLHNNGHTFISYAHLESFGVMGDVSTAMRDPVFYKWHSYIDRIFQEHKSRAYTENQLNYPGVSIAGIQVDRPNNLTTFWQQSDVDMSFTHLQHLPFTYTISLNAQRFGYVRIFMAPKNRDQRSMMIELDKFVTSLNPGPNTIRRRSTESSVIPFERTELEFNFCGCGWPNHMLVPKGLPEGLQCVLFIMVSND Anopheles_gambiae_tyr7 HRKDTHDLDLPTIIEVFYVDSKDYTASDLDEEHRLWYFREDIGVNLHHWHWHLVYPFDIVDKDRRGELFYYMHQQLVARYNFERFSNRLQRVKRLNLREPEGYFPKLDAWPGRVDASVLKDDVADLERWIDRIYEAIHQGFVDESGNRIPLDIDHLGNIIESSILSPNRQYGDMHNMGHVFISYAHLESFGVMGDVATAMRDPVFYRWHSYIDDIFQEHKNKPYTRSQLTFDGISITGITVQPPNTFQTFWQQSDVDLSFTHLQHSPFVTTIMIEAQRMAFVRVFLAPKNRDQRLFMIELDKFLVALRPGANRIRRRSKESTVIPFERTEAEFNFCGCGWPAHMLIPKGLPEGLPADLFIMVSND Anopheles_gambiae_tyr2 HRPDTKDLELPAFAQTFFIDSKKYTASDLDVEHRLWYFREDLGVNLHHWHWHLVYPIEIVDKDRRGELFYYMHQQIIARYNAERLSNHMARVQPFNLDEPEGYFPKMDAYPPRFDNTRLSDGIDDMKRWRERIYEAIHQGYVDTNNEKIVLDIDILGNIIEASDLTPNSTYGDFHNMGHILIAYSHLEYAGVMGDASTAMRDPIFYKWHAFIDNMFQEHKRLPYEKQELSFPDVRVESIQVEQVNRLTTFWQESDVDMSFTHLQHHEFSYTIKVEATRYGYVRIFLAPKLEQQRLMMVELDKFVVTMPPGSHTITRNSTESSVIPFERTELQNFLCGCGWPQHMLIPKGRPEGLRFELFVMVSND Anopheles_gambiae_tyr6 HRPDTKGLSIPTFAESFFMDPKNYTASDTEPEQRVAYFREDIGINLHHWHWHLVYPFDIVNKDRRGELFYYMHQQIIARYNVERMCNNLSRVRRYNFRAAEGYFPKLDAWPPRFAGTTIRDDVSELETWRDRFLQAIENMSVLPNGRQLPLDIDVLGNLMESSIISRNRPYGDLHNMGHVFISYSHLEQFGVMGDSATAMRDPVFYRWHAYIDDIFHLYKYKPYGNDRLDFPNIRVSSVSIETPNTLNTLWEQSTVDLGFTHLQHDEYNYVIEVNSSVMGMFRIFIAPTVDEQRKLMIELDKFSQGVKPGNNTIRRKSIDSSVIPYERTAAEFDFCGCGWPHHMLVPKGTTQGYPMVLFVMVSND Anopheles_gambiae_tyr3 HRPDTREVPITNISQIFFVEPSNYTASDREDEQRLAYFREDIGVNSHHWHWHLVYPTTVVNKDRRGELFYYMHHQILARYNVERFCNNLKKVQPLNLRVEEGYFPKILTYPARVTNQKLRDEISDVERWRDRVLAAIDQGYVDSSGNRIPLDIDILGNMIEASVLSINYNYGNLHNEGHNIISFAHLEEFGVMGDVTTAMRDPIFYRWHGFIDTVFNKFKTRPYNAGELNFDGITVDYIEAKKANTLLTYWQKSSADLAFTHLQNAPFTYTFNVTARRTGTCRIFICPKVEEQRLLAIEMDKFTVDLVPGENTIRRQSTESSVIPFERSLARFKFCGCGWPQHLLLPKGNAQGMVFDLFVMISDD Drosophila_melanogaster_tyr3 HRPDTKSVSVPSLLHLFFIDPANYTATDAEPEQRMAFFREDIGVNLHHWHWHLVYPASVVRKDRRGELFYYMHQQLLARYQIDRYAQGLGRIEPLNLREPEAYYPKLLTFCPRYPGMTISDRIADIESWLPRVLEAIDAGFASDDGVRVPLDIDVLGNILERSAISINRNYGDVHNMGHVLLAFIYLESSGVMGGVATAMRDPIFYRWHKFIDNIFLRNKARPYTMAELSNSNVTLEALETQAVNSFVTFWQRSQVDLRFTHLQCAPFVYRLRINSNRQDTVRIFLLPRQEDRRLLAIELDSFRVNLRPGMNNIVRQSSNSSVIPFERTNAQSRFCGCGWPAHMLLPKGNANGVEFDLFAMVSRD Bombyx_mori_tyr1 HRSDTSDVPVPSFLHLFFIDPANYTASDRVTEQRLAYFREDIGVNLHHWHWHLVYPAEVVRKDRRGELFYYMHQQMIARYQVERYSQGLGRVTPLNLRTPEPYYPKILTYPARYANMTLEDIISEVERQLQRIIAAIDEGVVAPSGQRTQLDIDILGNIVESSTISVNRQYGDTHNSGHVLLSLVFLESFGVMGDVTTAMRDPVFYRWHTFVDSIFQRHKQRPYGPAELRNPGVNLLSLETEVKNTLLTFWQRSQFDLGFTHLQHAAFNYRLQVATAKPATLRIFLAPKREEQRRLAIEMDTFRVNLTPGINNIIRRSANSSVIPYERTDANFRFCGCGWPSHMLVPKGDQFGVEYDLFAMLSDD Bombyx_mori_tyr2 HRDDTRDVEIPSFLELFFVDPANYTASDRVDEQRVAYWREDIGLSLHHWHWHLVYPSTVVRKDRRGELFYHMHQQTIARYNIERFANGLARTLSFQLRESEAYFPKIVAFSCRYPNQVMKDRLADMDVSIKRIFEAIDNGYAATNGDRVPLDIDLIGDLLEASTNSINFNYGDYHQNGHVMLGYIYLEGVGVMGDLTTTMRDPLFYRWHQHIDDIFVRHKQRAYTSSELSFNDITVDSFDVQPKNVLLTFWQRSQFDLGFTHIQHAPFSYRIQATSMRRGTVRLFLGPKVRDQRRHMVELDKFTVNLRPGQNSIVRRSDESNLIPYERTMEVFQFCNCGWPSHMLLPKGSASGLEYDFFVMISND Tribolium_castaneum_tyr2 HRTDTRDVEIPSFLELFYVDPANFTASDRVDEQRLAYWREDIGVNLHHWHWHLVYPARIVRKDRRGELFYYMHQQTMARYNIERFANGMPRVVAFNFREAEAYFPKITSYPARHPNETLSDSIADMELWTTRIFEAIDNGFASSSNQRVPLDIDLLGNIVEASTLSVNPQYGDLHNNGHNILGYIFLEGFGVVGDNTTAMRDPVFYRWHQHIDDIFVRHKQRAYTGQELAFNDVAVDSFEIQPVNILLTFWQRSQVNLGFTHIQHAPYSYRIRVNDTRRGTVRIFFGPKTREQRRLMVELDKFTVTLNAGANTIVRRSDQSSVIPYERTNEAFQFCNCGWPNHMLLPKGSPDGIEYDFFVMVSDD Tribolium_castaneum_tyr3 HRPDTKNLNIPSFFDLFFVDPTNYTASDREDEQRLAYFREDIGVNLHHWHWHLVYPGEVVNKDRRGELFYYMHQQLIARYNVDRFCNRLSRVRPLSLREPEGYFPKIVGFPARPQNTILRDSITDIELWGSRIAESIDGGYVAPGGNRIPLDIDVLGNIIEPSALSVNSQYGNYHGHMHNLISFSFLEGYGVVGEFQTAMRDPAFYRLHAQVDNMFHRYKRTPYNANQIGYAGVQIQSFGVQPANVLLTYWQRSQIDLGFTHLQHAPFTYRFAVNAARRGTCRIFIAPKTDEQRLLMIELDKFRVNLTPGVNNIVRRSEQSSVIPYERTTEQFRFCNCGWPHHLLLPKGTAEGMKFDLFLMISND Tribolium_castaneum_tyr1 HRPDTKDLNIPSFLELFFVDPSNYTASDREDEQRLAYFREDIGVNLHHWHWHLVYPGEVVNKDRRGELFYYMHQQLIARYNVERFCNRLARVRPLNLREPEGYFPKIIAFPPRPQNTVLRDTVSDLERSESRIAESIDGGYVGPGGNRIPLDIDVLGNIMEPSALSVNSQYGNYHGNLHNIIAYSFLEGYGVVGEFQTAMRDPSFYRLHAQVDNMFHRYKRTPYNANQLNYNGIQIQSLGVQPANVLLTYWQRSQVDLAFTHLQHAPFTFRLTVNATRRGTCRIFIGPKVDEQRLLMIELDKFTVNLNPGTNNIVRRSEQSSVIPYERTTEQFRFCNCGWPHHLLIPKGTPEGMQFDLFAMISND Drosophila_melanogaster_tyr2 HREDTKDVNIPSIVSLFFVDPANYTASDREDEQRMAYFREDIGVNMHHWHWHLVYPGDVVRKDRRGELFFYMHSQLIARYNADRFCAKLKKVRNLNYREPEGYYPKMISYPARAANTTLQDSVNDLERWRDRIHEAIDQGFVDKSGNRIMLDIDILGDVVEASSLTPNAQYGSLHNMGHNVIAYVYLEDYGVMGDVTTAMRDPIFYRWHGMIDGIFRRHKELPYTAEQLGNPGVTVNSVGVQPANVLLTYWQRSQVDLAFTHLQHAPFSFRVEVNAVRKGTLRIWLAPKSREQRRYFIEMDTSTVTLNPGMNTIVRRSDQSSVIPYERTLAQFRFCGCGWPQHMLVPKGSPEGVQFDLFAMVTDD Drosophila_melanogaster_tyr1 HRKDTGNVPVPSFLEMFFVDPASFSASEADPEQRLAYFREDIGVNLHHWHWHLVYPQEVVDKDRRGELFYYMHRQTVARYNVERFCNRLPAVKPLNLREPEAYFPKLLTYPGRHANMVLSHTILELESSLGRIKEAIQSGFAAADGTRVPLDIDILGNIMENSILSVNVPYGNYHSLGHVLIGFIYLEGHGVMGDFTTAMRDPTFYRFHGHVDDVFDMHKQKPYKAHELSFPGVSISDATVQARNRLLTFWQRTQVDLGFTHIQHAPFAYQIMVQEQKKGTVRIFLAPIYSQQRRYMLEMDKFVVKLHPGDNRIIRRSDQSSVIPYERTTESFRFCNCGWPDHMLLPKGHPDGQPFDLFIMISDD Anopheles_gambiae_tyr1 HRRDTRKVRVKNFAEVFFLDSQDYTATDLEEEHRLAYWREDIGINLHHYHWHLVYPFTIVAKDRRGELFFYMHQQVIARFNCERLCNSLKRVKKFNWREPEAYFPKLDGWPPRQSGMQWQDTIDEMERWRRNVEEAIATGTVLPNGQTRPLDIDTLGNMLESSALSPNREYGSIHNNGHSFTAYMYLEQFGVIADEATTMRDPFFYRWHAYIDDVFQKHKESPYTRSELENPGVQVRSVSVEQPNTLNTFWMLSDVNLSFTHLNYRHFSYRINVNSSRRTTVRIFITPKFSDQRKMCIEMDRFVTVLNAGENNIVRQSTESSIIPFEQTLATFNYCGCGWPQHMLVPKGTEAGMPFQLFVMLSND Daphnia_pulex_tyr QRQDSRSLRTPPIWEIFFFETRNFAATDRVVENKLSYFREDLGINSHHWHWHLIFPVEVNPPDRRGELFYYMHQQILARYDAERIANGLARVTSYDWDQPEAYFPKLTHWASRPSGLVLKDHIDDLQLWRTRILHAIHKGSVKGNGQVVHLDTNTLGELIEASQWSADKLYGDLHNFGHIAMCYIHSENMGVMGDSVTAMRDPIFYRWHKFIDSLFQQFKATPYSAQQLTLEGITVNSVEVHQKNLIITGWQESIVELDVTHLQHEDFSYRIQVTTSQDIVFRIFLAPIKREQRLLMIELDKFVARVTPGANLVKRKSDESSVIPFERTVKRTNFCGCGWPDHFLVPRGVPNGMPFTLFVMATSD Limulus_polyphemus_HcB QSPHTTNLLAPPIWQTMFFDQREPTGNNRDPEFKLSYFREDIAINSHHWHWHVIYPVGDKKINRKGELFYYMHEQMLARYDAERLCNGMRRVKSLDYDEIEGYYPRLHEYASRQANTRMMDTVIELERFRERIEHAISVGYILPDNTKTPLNIDILADLIEASNYSLNGAYGDLHNTGHVMLATAFNSSDGVMGFVQTALRDPLFYRWHKHIDNLLQNHKRTPYTDKELIADKIEIKEASITPKNKLYTFFDTKQLNLTITHLQHEEFTYNIKVNKDFTGTFRIFMAPKNNEQRILMIEMDKFQLKLSPGENNITRKSEDSNVLHKEMTPSSQHYCACGWPHHLLIPKGSAQGTAFHCFIMITDD Euphrynichus_bacillifer_HcA HRDDCKGVTVPPIQEIFFIPAEEETGNILDPEHTLAYYREDIGINAHHWHWHIAYPATGAVKDRKGELFFYMHQQMCARYDCERLSNGMNRMIPFNFEEHEGYAPHLTNYGSRPEGFSLRDDVQDMERWRERILESIHLGYVGHGEERIPLDTDILGAIIESSFESKNSTYGSLHNWGHVMMARMFQENPGVMSDTSTALRDPIFYRWHRFIDNIFQDYKATHYTKDDLSFDGIKVTDVVVKSDNVITTFMKEDELDLSYQHLDHEPFSISITVNAAKECIVRIFLAPQYEEGRRLFIELDKFKQTLAAGQSSFSRNAIDSNVLSKVPTDDYSEFCSCGWPENMLIPRGNHKGKPFVLFVLLTDD Mastigoproctus_giganteus_HcA HRDDCKGVHIPPIQEIFFIPAEEKTGNILDPEYKLAYYREDIETNAHHWHWHIVYPATGHIKDRKGELFYYMHQQMCARYDCERLSNGMNRMIPFNFEEKEGYAPHLIQYGARPQGFSLRDDVQSMERWRERIIEAIQLGYVDEHGEHVNLDADIIGALIESSHDSKNSRYGSLHNWGHVMMARMYQENPGVMSDTSTSLRDPIFYRWHRFVDNIFKDYKSTPYEKEEYSFDGIEVLEVTVKTDNVLTTFLKEDILELTYDHLDHEPFHYSIDVQATKEATVRIFLGPKYEDKRRLMIELDKFHKTLAPGKNTISRNSVDSSVVSHVPTANNQEYCSCGWPGHMLIPRGTRKGMDFHLYVVLTDD Limulus_polyphemus_HcA HRDDCRGVTVPPIQEVFFIPAEEQTGNILDSEYKVAYFREDIGINAHHWHWHIVYPTTHKVKDRKGELFYYMHQQMCARYDCERLSTELRRMIPFDFHQKEGYAPHLTNYASRPTGLSMSDDVQDMERWRERILDAIHGGFVDKEGNEVPLDLDMLGDLLESSYESVNREYGSLHNWGHVILAQVFKENPGVMSDTSTALRDPIFYRYHRFVDNIFQEYKISHYQKKDLDFPGVKVVNVTVNVPNVINTFLKESQLELSYHHLDHDPFTFSIGVEEVKNATVRVFLGPKYNEQRRFFIELDKFRATLEPGKTIITHKSSDSAVIDRTPTETNSEFCSCGWPQHMLIPRGNHRGMDFQLFVMLTDD Euphrynichus_bacillifer_HcB HRSDCDGIIVPPIQEIFFIPAEQETGNIFDPEYHLAYFREDIGANAHHWHWHIVYPGTHITKDRKGELFYYMHQQMCARYDCDRLSTGLRRLIPFNFHEEEGYNPHLTNYASRPAGLSMKDDVQDMIRWRERILDAIHIGFLDDHGNEIPLDTDLLADLMESSYESKNREYGSLHNWGHVIISQCFKENPGVMSDTSTSLRDPIFYRYHRFVDNIFQELKASPYKQSELDFTGIDVVNVTVNAPNLVHTFFAEDQLELRYHHLDHEPFTYNISVEAEKDSTVRIFLGPKYDEARRFYIELDKFHAKLSPGKNVVTRKSSESNVANKTPNASSDQFCSCGWPNYMLLPRGNHKGMEFELFVMLTDD Mastigoproctus_giganteus_HcB HRDDCKGLAVPPIQEIFFIPAEEETGNILNPEQRLAYFREDIEVNAHHWHWHLVFPATGKVKDRKGELFYYMHQQMCARYDCDRMSVGLQRMIPFNFEETEGYSAHLTHYASRPEGLHIRDSLQEMERWRERILEGINLGHVDDHGKEVELDIDILGALIESSHESKNEEYGSLHNWGHVMLARVFHENPGVMSDTSTSLRDPIFYRYHRFIDNMFQEYKASHYTKTELTFPEISISHVTIKVPNIIHTFMATDELELSYHHLNHEAFSYEIQVETVKHGTFRVFLAPKYNEQRRLFIELDKFHHGIHKGHNTIVRNSTESSVVSKIHTEKNTEYCSCGWPQHMLVPRGNEKGMDFQLFVMVTDD Epiperipatus_sp_Hc HRPDCKGVSLPPIQEIFFVTVQQTTGNILDPEYNLAYYREDIGINAHHWHWHLVYPATGKVKDRKGELFYYMHQQMCARYDCERLSNGMPRMEPFNFHEPEGYSSHLSPYPSRPDGMTLQDSVQDLERWRDRISDAIHIGHVDENGSHVPLDIDILGAMVEASYESINQAYGSIHNWGHVISARVYHLNPGVMSDTATSLRDPIFYRWHRFIDNMFQDYKETHYNHSDLEFPGIEITKVLLNHTNNINTFKEFSVLDLSFSHLNHEDFHYKIQVEKTKPATVRIFMAPKYKNLRRLMIEMDKFHAEIHPGHNTIVRHSKDSSVISSARSEHANEYCSCGWPDHLLVPRGDEKGMPFHLFVMLTDD Dictyostelium_fasciculatum_tyr HAPQFQSLQVPQALVIAVFCDQTIPKRWTNPDDLLKWWREDPMLNSHHWNWHTAYPSFAKLKDRQGELFVFMHRQMVARYDCERTALGIESLDPFTYKDSESFDPLLSTFVSRQSGSVMKDSLVDLEIWRQRLLEAIQKKTIASDGSMMTSEIADLGSSLEATMGSPNKAYGNLNKQAHNLMARVEQNNLGIMGDIIGAFRDPLFWRWHKHLDDFFHRFEIAPHKLEETAPPQFKVSKVSVKQENYLSTYMKSQIIDIKTYRLYHVPFNYEINVETFKKVVVRVYVVASDYGDRRKWVALDQFYTTLPEGQKTISRSSSESTILQRAVTTTLETYCKCGLPRNLLLPRGSKEGMKFKLCVVVTDD Polysphondylium_pallidum_tyr2 HSPHFQVLQVPQALVIAVFVDKNIPKRWRNPDALLKWWREDPMLNSHHWNWHTAYPSFAKLKDRQGELFVFMHRQMVARYDCERTALGLQPIDQFSYRESDAFDPLISMFVPRPADSKMRDSIVDLEIWRERLFEAIQKKSVQQDGTVTTTEIADLGSSLEATMGSPNKSYGNLNKQAHNLMSRVEQTSIGIMGDIIGAFRDPMFWRWHKHLDEFFHRFELTPYNIVDYAPANIRIANAVVRPENNLYTYMKTQIIAIKTNRLYYVPFNYEISVLKYKKVVVRVYIVASDYGDRRKWISLDQFFTALPEGQKTITRSSSESTILQQAATPSTETYCKCGLPRNLLLPRGTKEGMPFKIAVIVTDD Ciona_intestinalis_tyr1 HSKDAQQRFPPPLKNHPFFSTKICTADTLHGHALLSYWRDDYDLNDSHYYWHMVYRGAVGDFDRHGEVFLYVHSQMVARYETESLCWSLPLVRPWQYDDFNGYAPISSGYPPFSTWYSIRNPRARLEEWRDNIYAAIRKGQFTTSKDPLVLTLNFVGGILDAQYPSLDEEYGNLHNYGLGKFAEMEKSPYGLTISNFGAPRDPCFWRWYKHLQYYGRLAATRYPQDITAHRAEVVLSNLVVRLDGHITTFLGPPAVNFMKAKLGHEPYEWNVQVKNPQTLTLRLFIAAEDMNDYHSWIEMDRATVQLTDESATKVRLDTDSSVARKMGNRYASAVFRHGWPQNLMLPVGKVEGMPFVAFCIATDD Saccoglossus_kowaleksii_Hc HSKDAQQRFPPPLKNHPFFSTKICTADTLHGHALLSYWRDDYDLNDSHYYWHMVYRGAVGDFDRHGEVFLYVHSQMVARYETESLCWSLPLVRPWQYDDFNGYAPISSGYPPFSTWYSIRNPRARLEEWRDNIYAAIRKGQFTTSKDPLVLTLNFVGGILDAQYPSLDEEYGNLHNYGLGKFAEMEKSPYGLTISNFGAPRDPCFWRWYKHLQYYGRLAATRYPQDITAHRAEVVLSNLVVRLDGHITTFLGPPAVNFMKAKLGHEPYEWNVQVKNPQTLTLRLFIAAEDMNDYHSWIEMDRATVQLTDESATKVRLDTDSSVARKMGNRYASAVFRHGWPQNLMLPVGKVEGMPFVAFCIATDD Ciona_intestinalis_tyr2 HSKEAQYLVAPSLKEHLFAMPAPTTADTLKAIETLSYWREDYDLNDHHYHWHLVYPWSHRTIDRQGELFLYMHSQMLARYNAERLSWSIGLVDPWSYDEVPSYTPPPGARPPLQGWLEEHSSKDTMIFWRNNINKGIIQGYFTKKENKFNLTMNWVGIIVEAEAHQIDSDYGTLHNLGHDKFGEINKNRWGVMGFTSVAVRDPVFWIWHRHIDDFRQSIVKKQHALKESAPPHVKLTGVQILPDGGIATYLTAPQLGLHNAKLNHEPYKWVVKVENLKPFTVRIFIAPKQMHEQRRYIEMDKFLCTLTTKSATFVRLDVESSVARKVPDEYQDPRCLCGWPQNMMIPNGTELGIDYVVFAILTND Ciona_intestinalis_tyr4 HHSLARSNKVPEFTDAPDMSTHMVPPVGEPEEIWMDYWRHDADFVDHHRHWHRVYRARADHLDRQGELFVYMHRQMLARYNAEREAWGLEPVEPWEFTDVLGSDAGDEGIRPRPAGLKWSMDIRQFQVWTNNIRRAFRENIIPNQGAQSALQANWVGHIVEATSGTFYDNYGSLHNSGHGVFGQLQSGFSTYMATTAHAVRDHIFFRWHKFIDNLVEEYHQTQKTELGVDSPPVVIEENDIISSDLIETTLDLPQRQFEWGKLSHNAFNYHLRIRQELRLTFRIFICPAQANDRRRWIEMDKFRYILGAMETIITRQDVHSSVIRRFPQRTVSGFCECGWPYNLLLPRGKADGEKYLIAVLISDD Ciona_intestinalis_tyr3 HSKRAKSKQYPVPKPMDISNAAVTQRTGQPAETWMNYWRNDADLNYHHRHWHVVYVVGRPELFRQGELFGYMHAQMLARYNAERQSWRLPVVQAWQYNERVGYNTGFEGFSPRLPGSFPDREQTRFQRFERAIMRAINPPVVGETTRNVAMDANWAGHVIEASSSTWQAQLGSIHNNGHGVIGSMSRSGSSYMSATVTAMRDPIFYRWHKRIDNLWQEWSSRRVTDLQTDAPAVIIRPSDIIQSDDLQTYLGPPQKRYEDNKISHQPFTYHIRFQGELNLTVRIFICPASSNNRLSWIEMDKFVYRLGADATVISRPDRHSSVIKRERSTTATGFCECGWPYSMLLPRGTEQGEQWRLCVFLSDD Amphimedon_queenslandica_tyr HSKLCKKHRYPDPPKRDTQSAASGIGVGTPNELWMNYWRCDADFNFHHNHWHAVYRGGRNLKTRQGELFGYMHAQMLARFNADRETWGLEPVKAYEFDEVEGFDAGWEWIYPRPDKQIWPRIINENKHFEGEIEDLFDYGMIEYNGREQPLNSNFVGHILESSSGRWQRQFGGFHNMGHMAFVYTGNRNTTYMGTPLCAVRDPIFFRWHQHVDDLYQMWNDKVVTNLTKNSPDVIVDPCDVMSCGEIKTKLREADLAFEDYKLDHEPFSYHIRLKGELRLTLRLFICQERVNQRRRWIEMDKFVYVMPANATVVKRHDRESSVIKRSHAEIKAGNCDCGWPYTMLLPRGNKNGEKWLLGVYVSDD Aspergillus_nidulans_tyr2 HSKLCKKHRYPDPPKRDTQSAASGIGVGTPNELWMNYWRCDADFNFHHNHWHAVYRGGRNLKTRQGELFGYMHAQMLARFNADRETWGLEPVKAYEFDEVEGFDAGWEWIYPRPDKQIWPRIINENKHFEGEIEDLFDYGMIEYNGREQPLNSNFVGHILESSSGRWQRQFGGFHNMGHMAFVYTGNRNTTYMGTPLCAVRDPIFFRWHQHVDDLYQMWNDKVVTNLTKNSPDVIVDPCDVMSCGEIKTKLREADLAFEDYKLDHEPFSYHIRLKGELRLTLRLFICQERVNQRRRWIEMDKFVYVMPANATVVKRHDRESSVIKRSHAEIKAGNCDCGWPYTMLLPRGNKNGEKWLLGVYVSDD Aspergillus_nidulans_tyr1 HSKLCKKHRYPDPPKRDTQSAASGIGVGTPNELWMNYWRCDADFNFHHNHWHAVYRNGRNLKTRQGELFGYMHAQMLARFNADRETWGLEPVKAYEFDEVEGFDAGWEWIYPRPDKQIWPRIINENKHFEGEIEDLFDYGKIEYNGKEQPLNSNFVGHILESSSGRWQQQFGSFHNMGHMAFVYTGNRNTTYMGTPLCAVRDPIFFRWHQHVDDLYQMWNDKVLTNLTKNSPDVIIDPCDVMSCGEIKTKLREADLAFEDYKLDHEPFSYHIRLKGELRLTLRLFICQERVNKRRRWIEMDKFVYVMPANATVVKRQDRESSVIKRSHAEIKAGNCDCGWPYTMLLPRGNKNGEKWLLGVYVSDD ; END; BEGIN TREES; Title 'Beta tree_NJ'; LINK Taxa = Taxa2; TRANSLATE 1 Anopheles_gambiae_tyr5, 2 Anopheles_gambiae_tyr4, 3 Anopheles_gambiae_tyr9, 4 Anopheles_gambiae_tyr8, 5 Anopheles_gambiae_tyr7, 6 Anopheles_gambiae_tyr2, 7 Anopheles_gambiae_tyr6, 8 Anopheles_gambiae_tyr3, 9 Drosophila_melanogaster_tyr3, 10 Bombyx_mori_tyr1, 11 Bombyx_mori_tyr2, 12 Tribolium_castaneum_tyr2, 13 Tribolium_castaneum_tyr3, 14 Tribolium_castaneum_tyr1, 15 Drosophila_melanogaster_tyr2, 16 Drosophila_melanogaster_tyr1, 17 Anopheles_gambiae_tyr1, 18 Daphnia_pulex_tyr, 19 Limulus_polyphemus_HcB, 20 Euphrynichus_bacillifer_HcA, 21 Mastigoproctus_giganteus_HcA, 22 Limulus_polyphemus_HcA, 23 Euphrynichus_bacillifer_HcB, 24 Mastigoproctus_giganteus_HcB, 25 Epiperipatus_sp_Hc, 26 Dictyostelium_fasciculatum_tyr, 27 Polysphondylium_pallidum_tyr2, 28 Ciona_intestinalis_tyr1, 29 Saccoglossus_kowaleksii_Hc, 30 Ciona_intestinalis_tyr2, 31 Ciona_intestinalis_tyr4, 32 Ciona_intestinalis_tyr3, 33 Amphimedon_queenslandica_tyr, 34 Aspergillus_nidulans_tyr2, 35 Aspergillus_nidulans_tyr1; TREE tree_1 = ((26:0.148043,27:0.144522):0.37322,(((33:0.421537,(34:1.0E-6,35:1.0E-6):0.831261):0.443308,(28:0.429205,(29:0.533673,(30:0.017903,(31:1.0E-6,32:1.0E-6):0.008044):0.6238):0.018162):0.477959):0.231181,(25:0.516927,((19:0.249796,((20:0.137,21:0.195513):0.072018,(22:0.207161,(23:0.151938,24:0.175275):0.096127):0.0):0.07058):0.159241,(18:0.450521,(((10:0.343451,11:0.339851):0.0,((14:0.226379,(12:0.0,13:0.003247):0.139283):0.072033,(15:0.23511,(16:0.15483,17:0.18285):0.067959):0.027211):0.055801):0.025468,(9:0.298486,((6:0.199979,(7:0.078274,8:0.06061):0.208485):0.025409,((4:0.243437,5:0.225402):0.096142,(3:0.308068,(1:0.225987,2:0.113236):0.114784):0.007033):0.008612):0.022488):0.079372):0.1128):0.125751):0.00869):0.194737):0.37322); END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 365; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 365; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 365; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1362387445474; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 665703316062327991; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 479206847282436753; mqVersion 275; checksumv 0 3 4132934909 null getNumChars 365 numChars 365 getNumTaxa 35 numTaxa 35 short false bits 1048575 states 1048575 sumSquaresStatesOnly 1.94542527125722E14 sumSquares 1.94542527125722E14 longCompressibleToShort false usingShortMatrix false NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState true false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1280 966; setLocation 0 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #665703316062327991 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #665703316062327991; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -67; setLocation 0 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; endTell; showWindow; getEmployee #mesquite.lists.ColorTaxon.ColorTaxon; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #665703316062327991 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 7995.1362361709561.2379430447009730019; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -67; setLocation 0 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle on; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; setCornerMode Right_Angle 50; 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 on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; 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 on; 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 #479206847282436753 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -67; setLocation 0 22; 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; togglePaleInapplicable on; toggleShowBoldCellText off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables 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;