#NEXUS [written Mon Mar 04 18:32:32 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 Tribolium_castaneum_tyr2 Tribolium_castaneum_tyr3 Tribolium_castaneum_tyr1 Drosophila_melanogaster_tyr2 Drosophila_melanogaster_tyr1 Anopheles_gambiae_tyr1 Bombyx_mori_tyr1 Drosophila_melanogaster_tyr3 Anopheles_gambiae_tyr6 Anopheles_gambiae_tyr3 Anopheles_gambiae_tyr2 Anopheles_gambiae_tyr8 Anopheles_gambiae_tyr7 Anopheles_gambiae_tyr5 Anopheles_gambiae_tyr4 Anopheles_gambiae_tyr9 Daphnia_pulex_tyr Epiperipatus_sp_Hc Euphrynichus_bacillifer_HcB Mastigoproctus_giganteus_HcB Euphrynichus_bacillifer_HcA Mastigoproctus_giganteus_HcA Limulus_polyphemus_HcA Limulus_polyphemus_HcB Dictyostelium_fasciculatum_tyr Polysphondylium_pallidum_tyr2 Aspergillus_nidulans_tyr2 Aspergillus_nidulans_tyr1 Amphimedon_queenslandica_tyr Saccoglossus_kowaleksii_Hc Ciona_intestinalis_tyr1 'Ciona_intestinalis tyr4' Ciona_intestinalis_tyr3 Ciona_intestinalis_tyr2 Bombyx_mori_tyr2 ; END; BEGIN CHARACTERS; TITLE 'Matrix in file "alignment_betatype.nex"'; DIMENSIONS NCHAR=365; FORMAT DATATYPE = Protein GAP = - MISSING = ?; MATRIX Tribolium_castaneum_tyr2 HRQDTQDIDLPSFIESFYVDSKDYTASDLEEEHRLAYFREDLGINLHHWHWHLVYPFEVVAKNRRGELFYYMHQQIIARYNFERLCNKLKRATRFDFNEAEAYFPKLDAWPSRVANQKLRDDVEDLKRWSDRIYAAIHQGSVDERGRSITLTIDILGNMIESSILSPNRTYGDLHNMGHVFISYIHLESFGVMGDSATAMRDPIFYRWHSYIDDIFQEYKATRYTENQLNYPGITVSNIEVQSKNTFNTFWQQSDVDLSFTHLQHQPFTYKITVNGNRKGTCRIFLAPKTRDQKIMFIELDKFTVNLKQGQNTITRASSQSSVIPFERTLAQFNFCGCGWPQHMLIPKGTPEGMKSQLFVMISND Tribolium_castaneum_tyr3 HRQDTQDIDLPSFIESFYVDSKDYTASDLEEEHRLAYFREDLGINLHHWHWHLVYPFEVVAKNRRGELFYYMHQQIIARYNFERLCNKLKRATRFDFNEAEAYFPKLDAWPSRVANQKLRDDVEDLKRWSDRIYAAIHQGSVDERGRSITLTIDILGNMIESSILSPNRTYGDLHNMGHVFISYIHLESFGVMGDSATAMRDPIFYRWHSYIDDIFQEYKATRYTENQLNYPGITVSNIEVPSKNTFNTFWQQSDVDLSFTHLQHQPFTYKITVNGNRKGTCRIFLAPKTRDQKIMFIELDKFTVNLKQGQNTITRASSQSSVIPFERTLAQFNFCGCGWPQHMLIPKGTPEGMKSQLFVMISND Tribolium_castaneum_tyr1 HRPDTQNLDLPSFIHVFYVDSQDFTASDLDEEHRVAYWREDIGLNLHHWHWHLVYPFEIVDKNRRGEIFYYMHQQIIARFNIERLCNGLKRVVKLNWREPEAYFPKLDTWPARPVNQVPRDSLDDMDRWRDRIYDAIHSGVVGDNGQNIPLTIDVLGNIIESSILSPNRNYGDFHNMGHILIGYIFLEPFGVMADPAVDLRDPLFFRWHAYIDDMFQEFKATRYTVAQLNYPGVTVTNIEVQKPNVLSTFWQQSDLDLSFTHLQNQDFTYKITVNNNRMGTCRIFLAPQFRNQKDMFIELDRFAVSLKQGTNTITRHSTESSLIPFERTLSEFNFCGCGWPQHMLLPKGTEAGYPCHLFVMISND Drosophila_melanogaster_tyr2 HRPDTQGLDLPSFSQTFFIDSQDYTASDLDPEHRLWYFREDLGINLHHWHWHLVYPFEIVAKDRRGELFYYMHQQVIARYNAERFSNNLARVLPFNLRDPEGYFPKMDAWPPRFESTRLSDEIGDLERWRDRIYEAIHQGFVDERGNRVPLDIDTLGNMIESSILSPNRVYGDLHNNGHTFISYAHLESFGVMGDVSTAMRDPVFYKWHSYIDRIFQEHKSRAYTENQLNYPGVSIAGIQVDRPNNLTTFWQQSDVDMSFTHLQHLPFTYTISLNAQRFGYVRIFMAPKNRDQRSMMIELDKFVTSLNPGPNTIRRRSTESSVIPFERTELEFNFCGCGWPNHMLVPKGLPEGLQCVLFIMVSND Drosophila_melanogaster_tyr1 HRKDTHDLDLPTIIEVFYVDSKDYTASDLDEEHRLWYFREDIGVNLHHWHWHLVYPFDIVDKDRRGELFYYMHQQLVARYNFERFSNRLQRVKRLNLREPEGYFPKLDAWPGRVDASVLKDDVADLERWIDRIYEAIHQGFVDESGNRIPLDIDHLGNIIESSILSPNRQYGDMHNMGHVFISYAHLESFGVMGDVATAMRDPVFYRWHSYIDDIFQEHKNKPYTRSQLTFDGISITGITVQPPNTFQTFWQQSDVDLSFTHLQHSPFVTTIMIEAQRMAFVRVFLAPKNRDQRLFMIELDKFLVALRPGANRIRRRSKESTVIPFERTEAEFNFCGCGWPAHMLIPKGLPEGLPADLFIMVSND Anopheles_gambiae_tyr1 HRPDTKDLELPAFAQTFFIDSKKYTASDLDVEHRLWYFREDLGVNLHHWHWHLVYPIEIVDKDRRGELFYYMHQQIIARYNAERLSNHMARVQPFNLDEPEGYFPKMDAYPPRFDNTRLSDGIDDMKRWRERIYEAIHQGYVDTNNEKIVLDIDILGNIIEASDLTPNSTYGDFHNMGHILIAYSHLEYAGVMGDASTAMRDPIFYKWHAFIDNMFQEHKRLPYEKQELSFPDVRVESIQVEQVNRLTTFWQESDVDMSFTHLQHHEFSYTIKVEATRYGYVRIFLAPKLEQQRLMMVELDKFVVTMPPGSHTITRNSTESSVIPFERTELQNFLCGCGWPQHMLIPKGRPEGLRFELFVMVSND Bombyx_mori_tyr1 HRPDTKGLSIPTFAESFFMDPKNYTASDTEPEQRVAYFREDIGINLHHWHWHLVYPFDIVNKDRRGELFYYMHQQIIARYNVERMCNNLSRVRRYNFRAAEGYFPKLDAWPPRFAGTTIRDDVSELETWRDRFLQAIENMSVLPNGRQLPLDIDVLGNLMESSIISRNRPYGDLHNMGHVFISYSHLEQFGVMGDSATAMRDPVFYRWHAYIDDIFHLYKYKPYGNDRLDFPNIRVSSVSIETPNTLNTLWEQSTVDLGFTHLQHDEYNYVIEVNSSVMGMFRIFIAPTVDEQRKLMIELDKFSQGVKPGNNTIRRKSIDSSVIPYERTAAEFDFCGCGWPHHMLVPKGTTQGYPMVLFVMVSND Drosophila_melanogaster_tyr3 HRPDTREVPITNISQIFFVEPSNYTASDREDEQRLAYFREDIGVNSHHWHWHLVYPTTVVNKDRRGELFYYMHHQILARYNVERFCNNLKKVQPLNLRVEEGYFPKILTYPARVTNQKLRDEISDVERWRDRVLAAIDQGYVDSSGNRIPLDIDILGNMIEASVLSINYNYGNLHNEGHNIISFAHLEEFGVMGDVTTAMRDPIFYRWHGFIDTVFNKFKTRPYNAGELNFDGITVDYIEAKKANTLLTYWQKSSADLAFTHLQNAPFTYTFNVTARRTGTCRIFICPKVEEQRLLAIEMDKFTVDLVPGENTIRRQSTESSVIPFERSLARFKFCGCGWPQHLLLPKGNAQGMVFDLFVMISDD Anopheles_gambiae_tyr6 HRPDTKSVSVPSLLHLFFIDPANYTATDAEPEQRMAFFREDIGVNLHHWHWHLVYPASVVRKDRRGELFYYMHQQLLARYQIDRYAQGLGRIEPLNLREPEAYYPKLLTFCPRYPGMTISDRIADIESWLPRVLEAIDAGFASDDGVRVPLDIDVLGNILERSAISINRNYGDVHNMGHVLLAFIYLESSGVMGGVATAMRDPIFYRWHKFIDNIFLRNKARPYTMAELSNSNVTLEALETQAVNSFVTFWQRSQVDLRFTHLQCAPFVYRLRINSNRQDTVRIFLLPRQEDRRLLAIELDSFRVNLRPGMNNIVRQSSNSSVIPFERTNAQSRFCGCGWPAHMLLPKGNANGVEFDLFAMVSRD Anopheles_gambiae_tyr3 HRSDTSDVPVPSFLHLFFIDPANYTASDRVTEQRLAYFREDIGVNLHHWHWHLVYPAEVVRKDRRGELFYYMHQQMIARYQVERYSQGLGRVTPLNLRTPEPYYPKILTYPARYANMTLEDIISEVERQLQRIIAAIDEGVVAPSGQRTQLDIDILGNIVESSTISVNRQYGDTHNSGHVLLSLVFLESFGVMGDVTTAMRDPVFYRWHTFVDSIFQRHKQRPYGPAELRNPGVNLLSLETEVKNTLLTFWQRSQFDLGFTHLQHAAFNYRLQVATAKPATLRIFLAPKREEQRRLAIEMDTFRVNLTPGINNIIRRSANSSVIPYERTDANFRFCGCGWPSHMLVPKGDQFGVEYDLFAMLSDD Anopheles_gambiae_tyr2 HRDDTRDVEIPSFLELFFVDPANYTASDRVDEQRVAYWREDIGLSLHHWHWHLVYPSTVVRKDRRGELFYHMHQQTIARYNIERFANGLARTLSFQLRESEAYFPKIVAFSCRYPNQVMKDRLADMDVSIKRIFEAIDNGYAATNGDRVPLDIDLIGDLLEASTNSINFNYGDYHQNGHVMLGYIYLEGVGVMGDLTTTMRDPLFYRWHQHIDDIFVRHKQRAYTSSELSFNDITVDSFDVQPKNVLLTFWQRSQFDLGFTHIQHAPFSYRIQATSMRRGTVRLFLGPKVRDQRRHMVELDKFTVNLRPGQNSIVRRSDESNLIPYERTMEVFQFCNCGWPSHMLLPKGSASGLEYDFFVMISND Anopheles_gambiae_tyr8 HRTDTRDVEIPSFLELFYVDPANFTASDRVDEQRLAYWREDIGVNLHHWHWHLVYPARIVRKDRRGELFYYMHQQTMARYNIERFANGMPRVVAFNFREAEAYFPKITSYPARHPNETLSDSIADMELWTTRIFEAIDNGFASSSNQRVPLDIDLLGNIVEASTLSVNPQYGDLHNNGHNILGYIFLEGFGVVGDNTTAMRDPVFYRWHQHIDDIFVRHKQRAYTGQELAFNDVAVDSFEIQPVNILLTFWQRSQVNLGFTHIQHAPYSYRIRVNDTRRGTVRIFFGPKTREQRRLMVELDKFTVTLNAGANTIVRRSDQSSVIPYERTNEAFQFCNCGWPNHMLLPKGSPDGIEYDFFVMVSDD Anopheles_gambiae_tyr7 HRPDTKNLNIPSFFDLFFVDPTNYTASDREDEQRLAYFREDIGVNLHHWHWHLVYPGEVVNKDRRGELFYYMHQQLIARYNVDRFCNRLSRVRPLSLREPEGYFPKIVGFPARPQNTILRDSITDIELWGSRIAESIDGGYVAPGGNRIPLDIDVLGNIIEPSALSVNSQYGNYHGHMHNLISFSFLEGYGVVGEFQTAMRDPAFYRLHAQVDNMFHRYKRTPYNANQIGYAGVQIQSFGVQPANVLLTYWQRSQIDLGFTHLQHAPFTYRFAVNAARRGTCRIFIAPKTDEQRLLMIELDKFRVNLTPGVNNIVRRSEQSSVIPYERTTEQFRFCNCGWPHHLLLPKGTAEGMKFDLFLMISND Anopheles_gambiae_tyr5 HRPDTKDLNIPSFLELFFVDPSNYTASDREDEQRLAYFREDIGVNLHHWHWHLVYPGEVVNKDRRGELFYYMHQQLIARYNVERFCNRLARVRPLNLREPEGYFPKIIAFPPRPQNTVLRDTVSDLERSESRIAESIDGGYVGPGGNRIPLDIDVLGNIMEPSALSVNSQYGNYHGNLHNIIAYSFLEGYGVVGEFQTAMRDPSFYRLHAQVDNMFHRYKRTPYNANQLNYNGIQIQSLGVQPANVLLTYWQRSQVDLAFTHLQHAPFTFRLTVNATRRGTCRIFIGPKVDEQRLLMIELDKFTVNLNPGTNNIVRRSEQSSVIPYERTTEQFRFCNCGWPHHLLIPKGTPEGMQFDLFAMISND Anopheles_gambiae_tyr4 HREDTKDVNIPSIVSLFFVDPANYTASDREDEQRMAYFREDIGVNMHHWHWHLVYPGDVVRKDRRGELFFYMHSQLIARYNADRFCAKLKKVRNLNYREPEGYYPKMISYPARAANTTLQDSVNDLERWRDRIHEAIDQGFVDKSGNRIMLDIDILGDVVEASSLTPNAQYGSLHNMGHNVIAYVYLEDYGVMGDVTTAMRDPIFYRWHGMIDGIFRRHKELPYTAEQLGNPGVTVNSVGVQPANVLLTYWQRSQVDLAFTHLQHAPFSFRVEVNAVRKGTLRIWLAPKSREQRRYFIEMDTSTVTLNPGMNTIVRRSDQSSVIPYERTLAQFRFCGCGWPQHMLVPKGSPEGVQFDLFAMVTDD Anopheles_gambiae_tyr9 HRKDTGNVPVPSFLEMFFVDPASFSASEADPEQRLAYFREDIGVNLHHWHWHLVYPQEVVDKDRRGELFYYMHRQTVARYNVERFCNRLPAVKPLNLREPEAYFPKLLTYPGRHANMVLSHTILELESSLGRIKEAIQSGFAAADGTRVPLDIDILGNIMENSILSVNVPYGNYHSLGHVLIGFIYLEGHGVMGDFTTAMRDPTFYRFHGHVDDVFDMHKQKPYKAHELSFPGVSISDATVQARNRLLTFWQRTQVDLGFTHIQHAPFAYQIMVQEQKKGTVRIFLAPIYSQQRRYMLEMDKFVVKLHPGDNRIIRRSDQSSVIPYERTTESFRFCNCGWPDHMLLPKGHPDGQPFDLFIMISDD Daphnia_pulex_tyr QRQDSRSLRTPPIWEIFFFETRNFAATDRVVENKLSYFREDLGINSHHWHWHLIFPVEVNPPDRRGELFYYMHQQILARYDAERIANGLARVTSYDWDQPEAYFPKLTHWASRPSGLVLKDHIDDLQLWRTRILHAIHKGSVKGNGQVVHLDTNTLGELIEASQWSADKLYGDLHNFGHIAMCYIHSENMGVMGDSVTAMRDPIFYRWHKFIDSLFQQFKATPYSAQQLTLEGITVNSVEVHQKNLIITGWQESIVELDVTHLQHEDFSYRIQVTTSQDIVFRIFLAPIKREQRLLMIELDKFVARVTPGANLVKRKSDESSVIPFERTVKRTNFCGCGWPDHFLVPRGVPNGMPFTLFVMATSD Epiperipatus_sp_Hc QSPHTTNLLAPPIWQTMFFDQREPTGNNRDPEFKLSYFREDIAINSHHWHWHVIYPVGDKKINRKGELFYYMHEQMLARYDAERLCNGMRRVKSLDYDEIEGYYPRLHEYASRQANTRMMDTVIELERFRERIEHAISVGYILPDNTKTPLNIDILADLIEASNYSLNGAYGDLHNTGHVMLATAFNSSDGVMGFVQTALRDPLFYRWHKHIDNLLQNHKRTPYTDKELIADKIEIKEASITPKNKLYTFFDTKQLNLTITHLQHEEFTYNIKVNKDFTGTFRIFMAPKNNEQRILMIEMDKFQLKLSPGENNITRKSEDSNVLHKEMTPSSQHYCACGWPHHLLIPKGSAQGTAFHCFIMITDD Euphrynichus_bacillifer_HcB QSPHTTNLLAPPIWQTMFFDQREPTGNNRDPEFKLSYFREDIAINSHHWHWHVIYPVGDKKINRKGELFYYMHEQMLARYDAERLCNGMRRVKSLDYDEIEGYYPRLHEYASRQANTRMMDTVIELERFRERIEHAISVGYILPDNTKTPLNIDILADLIEASNYSLNGAYGDLHNTGHVMLATAFNSSDGVMGFVQTALRDPLFYRWHKHIDNLLQNHKRTPYTDKELIADKIEIKEASITPKNKLYTFFDTKQLNLTITHLQHEEFTYNIKVNKDFTGTFRIFMAPKNNEQRILMIEMDKFQLKLSPGENNITRKSEDSNVLHKEMTPSSQHYCACGWPHHLLIPKGSAQGTAFHCFIMITDD Mastigoproctus_giganteus_HcB HRDDCKGVTVPPIQEIFFIPAEEETGNILDPEHTLAYYREDIGINAHHWHWHIAYPATGAVKDRKGELFFYMHQQMCARYDCERLSNGMNRMIPFNFEEHEGYAPHLTNYGSRPEGFSLRDDVQDMERWRERILESIHLGYVGHGEERIPLDTDILGAIIESSFESKNSTYGSLHNWGHVMMARMFQENPGVMSDTSTALRDPIFYRWHRFIDNIFQDYKATHYTKDDLSFDGIKVTDVVVKSDNVITTFMKEDELDLSYQHLDHEPFSISITVNAAKECIVRIFLAPQYEEGRRLFIELDKFKQTLAAGQSSFSRNAIDSNVLSKVPTDDYSEFCSCGWPENMLIPRGNHKGKPFVLFVLLTDD Euphrynichus_bacillifer_HcA HRDDCKGVHIPPIQEIFFIPAEEKTGNILDPEYKLAYYREDIETNAHHWHWHIVYPATGHIKDRKGELFYYMHQQMCARYDCERLSNGMNRMIPFNFEEKEGYAPHLIQYGARPQGFSLRDDVQSMERWRERIIEAIQLGYVDEHGEHVNLDADIIGALIESSHDSKNSRYGSLHNWGHVMMARMYQENPGVMSDTSTSLRDPIFYRWHRFVDNIFKDYKSTPYEKEEYSFDGIEVLEVTVKTDNVLTTFLKEDILELTYDHLDHEPFHYSIDVQATKEATVRIFLGPKYEDKRRLMIELDKFHKTLAPGKNTISRNSVDSSVVSHVPTANNQEYCSCGWPGHMLIPRGTRKGMDFHLYVVLTDD Mastigoproctus_giganteus_HcA HRDDCRGVTVPPIQEVFFIPAEEQTGNILDSEYKVAYFREDIGINAHHWHWHIVYPTTHKVKDRKGELFYYMHQQMCARYDCERLSTELRRMIPFDFHQKEGYAPHLTNYASRPTGLSMSDDVQDMERWRERILDAIHGGFVDKEGNEVPLDLDMLGDLLESSYESVNREYGSLHNWGHVILAQVFKENPGVMSDTSTALRDPIFYRYHRFVDNIFQEYKISHYQKKDLDFPGVKVVNVTVNVPNVINTFLKESQLELSYHHLDHDPFTFSIGVEEVKNATVRVFLGPKYNEQRRFFIELDKFRATLEPGKTIITHKSSDSAVIDRTPTETNSEFCSCGWPQHMLIPRGNHRGMDFQLFVMLTDD Limulus_polyphemus_HcA HRSDCDGIIVPPIQEIFFIPAEQETGNIFDPEYHLAYFREDIGANAHHWHWHIVYPGTHITKDRKGELFYYMHQQMCARYDCDRLSTGLRRLIPFNFHEEEGYNPHLTNYASRPAGLSMKDDVQDMIRWRERILDAIHIGFLDDHGNEIPLDTDLLADLMESSYESKNREYGSLHNWGHVIISQCFKENPGVMSDTSTSLRDPIFYRYHRFVDNIFQELKASPYKQSELDFTGIDVVNVTVNAPNLVHTFFAEDQLELRYHHLDHEPFTYNISVEAEKDSTVRIFLGPKYDEARRFYIELDKFHAKLSPGKNVVTRKSSESNVANKTPNASSDQFCSCGWPNYMLLPRGNHKGMEFELFVMLTDD Limulus_polyphemus_HcB HRDDCKGLAVPPIQEIFFIPAEEETGNILNPEQRLAYFREDIEVNAHHWHWHLVFPATGKVKDRKGELFYYMHQQMCARYDCDRMSVGLQRMIPFNFEETEGYSAHLTHYASRPEGLHIRDSLQEMERWRERILEGINLGHVDDHGKEVELDIDILGALIESSHESKNEEYGSLHNWGHVMLARVFHENPGVMSDTSTSLRDPIFYRYHRFIDNMFQEYKASHYTKTELTFPEISISHVTIKVPNIIHTFMATDELELSYHHLNHEAFSYEIQVETVKHGTFRVFLAPKYNEQRRLFIELDKFHHGIHKGHNTIVRNSTESSVVSKIHTEKNTEYCSCGWPQHMLVPRGNEKGMDFQLFVMVTDD Dictyostelium_fasciculatum_tyr HRPDCKGVSLPPIQEIFFVTVQQTTGNILDPEYNLAYYREDIGINAHHWHWHLVYPATGKVKDRKGELFYYMHQQMCARYDCERLSNGMPRMEPFNFHEPEGYSSHLSPYPSRPDGMTLQDSVQDLERWRDRISDAIHIGHVDENGSHVPLDIDILGAMVEASYESINQAYGSIHNWGHVISARVYHLNPGVMSDTATSLRDPIFYRWHRFIDNMFQDYKETHYNHSDLEFPGIEITKVLLNHTNNINTFKEFSVLDLSFSHLNHEDFHYKIQVEKTKPATVRIFMAPKYKNLRRLMIEMDKFHAEIHPGHNTIVRHSKDSSVISSARSEHANEYCSCGWPDHLLVPRGDEKGMPFHLFVMLTDD Polysphondylium_pallidum_tyr2 HAPQFQSLQVPQALVIAVFCDQTIPKRWTNPDDLLKWWREDPMLNSHHWNWHTAYPSFAKLKDRQGELFVFMHRQMVARYDCERTALGIESLDPFTYKDSESFDPLLSTFVSRQSGSVMKDSLVDLEIWRQRLLEAIQKKTIASDGSMMTSEIADLGSSLEATMGSPNKAYGNLNKQAHNLMARVEQNNLGIMGDIIGAFRDPLFWRWHKHLDDFFHRFEIAPHKLEETAPPQFKVSKVSVKQENYLSTYMKSQIIDIKTYRLYHVPFNYEINVETFKKVVVRVYVVASDYGDRRKWVALDQFYTTLPEGQKTISRSSSESTILQRAVTTTLETYCKCGLPRNLLLPRGSKEGMKFKLCVVVTDD Aspergillus_nidulans_tyr2 HSPHFQVLQVPQALVIAVFVDKNIPKRWRNPDALLKWWREDPMLNSHHWNWHTAYPSFAKLKDRQGELFVFMHRQMVARYDCERTALGLQPIDQFSYRESDAFDPLISMFVPRPADSKMRDSIVDLEIWRERLFEAIQKKSVQQDGTVTTTEIADLGSSLEATMGSPNKSYGNLNKQAHNLMSRVEQTSIGIMGDIIGAFRDPMFWRWHKHLDEFFHRFELTPYNIVDYAPANIRIANAVVRPENNLYTYMKTQIIAIKTNRLYYVPFNYEISVLKYKKVVVRVYIVASDYGDRRKWISLDQFFTALPEGQKTITRSSSESTILQQAATPSTETYCKCGLPRNLLLPRGTKEGMPFKIAVIVTDD Aspergillus_nidulans_tyr1 HSKDAQQRFPPPLKNHPFFSTKICTADTLHGHALLSYWRDDYDLNDSHYYWHMVYRGAVGDFDRHGEVFLYVHSQMVARYETESLCWSLPLVRPWQYDDFNGYAPISSGYPPFSTWYSIRNPRARLEEWRDNIYAAIRKGQFTTSKDPLVLTLNFVGGILDAQYPSLDEEYGNLHNYGLGKFAEMEKSPYGLTISNFGAPRDPCFWRWYKHLQYYGRLAATRYPQDITAHRAEVVLSNLVVRLDGHITTFLGPPAVNFMKAKLGHEPYEWNVQVKNPQTLTLRLFIAAEDMNDYHSWIEMDRATVQLTDESATKVRLDTDSSVARKMGNRYASAVFRHGWPQNLMLPVGKVEGMPFVAFCIATDD Amphimedon_queenslandica_tyr HSKDAQQRFPPPLKNHPFFSTKICTADTLHGHALLSYWRDDYDLNDSHYYWHMVYRGAVGDFDRHGEVFLYVHSQMVARYETESLCWSLPLVRPWQYDDFNGYAPISSGYPPFSTWYSIRNPRARLEEWRDNIYAAIRKGQFTTSKDPLVLTLNFVGGILDAQYPSLDEEYGNLHNYGLGKFAEMEKSPYGLTISNFGAPRDPCFWRWYKHLQYYGRLAATRYPQDITAHRAEVVLSNLVVRLDGHITTFLGPPAVNFMKAKLGHEPYEWNVQVKNPQTLTLRLFIAAEDMNDYHSWIEMDRATVQLTDESATKVRLDTDSSVARKMGNRYASAVFRHGWPQNLMLPVGKVEGMPFVAFCIATDD Saccoglossus_kowaleksii_Hc HSKEAQYLVAPSLKEHLFAMPAPTTADTLKAIETLSYWREDYDLNDHHYHWHLVYPWSHRTIDRQGELFLYMHSQMLARYNAERLSWSIGLVDPWSYDEVPSYTPPPGARPPLQGWLEEHSSKDTMIFWRNNINKGIIQGYFTKKENKFNLTMNWVGIIVEAEAHQIDSDYGTLHNLGHDKFGEINKNRWGVMGFTSVAVRDPVFWIWHRHIDDFRQSIVKKQHALKESAPPHVKLTGVQILPDGGIATYLTAPQLGLHNAKLNHEPYKWVVKVENLKPFTVRIFIAPKQMHEQRRYIEMDKFLCTLTTKSATFVRLDVESSVARKVPDEYQDPRCLCGWPQNMMIPNGTELGIDYVVFAILTND Ciona_intestinalis_tyr1 HHSLARSNKVPEFTDAPDMSTHMVPPVGEPEEIWMDYWRHDADFVDHHRHWHRVYRARADHLDRQGELFVYMHRQMLARYNAEREAWGLEPVEPWEFTDVLGSDAGDEGIRPRPAGLKWSMDIRQFQVWTNNIRRAFRENIIPNQGAQSALQANWVGHIVEATSGTFYDNYGSLHNSGHGVFGQLQSGFSTYMATTAHAVRDHIFFRWHKFIDNLVEEYHQTQKTELGVDSPPVVIEENDIISSDLIETTLDLPQRQFEWGKLSHNAFNYHLRIRQELRLTFRIFICPAQANDRRRWIEMDKFRYILGAMETIITRQDVHSSVIRRFPQRTVSGFCECGWPYNLLLPRGKADGEKYLIAVLISDD 'Ciona_intestinalis tyr4' HSKRAKSKQYPVPKPMDISNAAVTQRTGQPAETWMNYWRNDADLNYHHRHWHVVYVVGRPELFRQGELFGYMHAQMLARYNAERQSWRLPVVQAWQYNERVGYNTGFEGFSPRLPGSFPDREQTRFQRFERAIMRAINPPVVGETTRNVAMDANWAGHVIEASSSTWQAQLGSIHNNGHGVIGSMSRSGSSYMSATVTAMRDPIFYRWHKRIDNLWQEWSSRRVTDLQTDAPAVIIRPSDIIQSDDLQTYLGPPQKRYEDNKISHQPFTYHIRFQGELNLTVRIFICPASSNNRLSWIEMDKFVYRLGADATVISRPDRHSSVIKRERSTTATGFCECGWPYSMLLPRGTEQGEQWRLCVFLSDD Ciona_intestinalis_tyr3 HSKLCKKHRYPDPPKRDTQSAASGIGVGTPNELWMNYWRCDADFNFHHNHWHAVYRGGRNLKTRQGELFGYMHAQMLARFNADRETWGLEPVKAYEFDEVEGFDAGWEWIYPRPDKQIWPRIINENKHFEGEIEDLFDYGMIEYNGREQPLNSNFVGHILESSSGRWQRQFGGFHNMGHMAFVYTGNRNTTYMGTPLCAVRDPIFFRWHQHVDDLYQMWNDKVVTNLTKNSPDVIVDPCDVMSCGEIKTKLREADLAFEDYKLDHEPFSYHIRLKGELRLTLRLFICQERVNQRRRWIEMDKFVYVMPANATVVKRHDRESSVIKRSHAEIKAGNCDCGWPYTMLLPRGNKNGEKWLLGVYVSDD Ciona_intestinalis_tyr2 HSKLCKKHRYPDPPKRDTQSAASGIGVGTPNELWMNYWRCDADFNFHHNHWHAVYRGGRNLKTRQGELFGYMHAQMLARFNADRETWGLEPVKAYEFDEVEGFDAGWEWIYPRPDKQIWPRIINENKHFEGEIEDLFDYGMIEYNGREQPLNSNFVGHILESSSGRWQRQFGGFHNMGHMAFVYTGNRNTTYMGTPLCAVRDPIFFRWHQHVDDLYQMWNDKVVTNLTKNSPDVIVDPCDVMSCGEIKTKLREADLAFEDYKLDHEPFSYHIRLKGELRLTLRLFICQERVNQRRRWIEMDKFVYVMPANATVVKRHDRESSVIKRSHAEIKAGNCDCGWPYTMLLPRGNKNGEKWLLGVYVSDD Bombyx_mori_tyr2 HSKLCKKHRYPDPPKRDTQSAASGIGVGTPNELWMNYWRCDADFNFHHNHWHAVYRNGRNLKTRQGELFGYMHAQMLARFNADRETWGLEPVKAYEFDEVEGFDAGWEWIYPRPDKQIWPRIINENKHFEGEIEDLFDYGKIEYNGKEQPLNSNFVGHILESSSGRWQQQFGSFHNMGHMAFVYTGNRNTTYMGTPLCAVRDPIFFRWHQHVDDLYQMWNDKVLTNLTKNSPDVIIDPCDVMSCGEIKTKLREADLAFEDYKLDHEPFSYHIRLKGELRLTLRLFICQERVNKRRRWIEMDKFVYVMPANATVVKRQDRESSVIKRSHAEIKAGNCDCGWPYTMLLPRGNKNGEKWLLGVYVSDD ; END; BEGIN TREES; Title 'Beta subclass_BI tree'; LINK Taxa = Taxa2; TRANSLATE 1 Tribolium_castaneum_tyr2, 2 Tribolium_castaneum_tyr3, 3 Tribolium_castaneum_tyr1, 4 Drosophila_melanogaster_tyr2, 5 Drosophila_melanogaster_tyr1, 6 Anopheles_gambiae_tyr1, 7 Bombyx_mori_tyr1, 8 Drosophila_melanogaster_tyr3, 9 Anopheles_gambiae_tyr6, 10 Anopheles_gambiae_tyr3, 11 Anopheles_gambiae_tyr2, 12 Anopheles_gambiae_tyr8, 13 Anopheles_gambiae_tyr7, 14 Anopheles_gambiae_tyr5, 15 Anopheles_gambiae_tyr4, 16 Anopheles_gambiae_tyr9, 17 Daphnia_pulex_tyr, 18 Epiperipatus_sp_Hc, 19 Euphrynichus_bacillifer_HcB, 20 Mastigoproctus_giganteus_HcB, 21 Euphrynichus_bacillifer_HcA, 22 Mastigoproctus_giganteus_HcA, 23 Limulus_polyphemus_HcA, 24 Limulus_polyphemus_HcB, 25 Dictyostelium_fasciculatum_tyr, 26 Polysphondylium_pallidum_tyr2, 27 Aspergillus_nidulans_tyr2, 28 Aspergillus_nidulans_tyr1, 29 Amphimedon_queenslandica_tyr, 30 Saccoglossus_kowaleksii_Hc, 31 Ciona_intestinalis_tyr1, 32 'Ciona_intestinalis tyr4', 33 Ciona_intestinalis_tyr3, 34 Ciona_intestinalis_tyr2, 35 Bombyx_mori_tyr2; TREE con_50_majrule = ((25:0.14049,26:0.120643):0.3994105,(((29:0.522012,(27:0.001612,28:0.001589):0.789252):0.415548,(30:0.43284,(31:0.436223,(34:0.013545,(32:0.001651,33:0.001707):0.011969):0.58256):0.16445):0.660148):0.357998,((24:0.188878,(23:0.157183,((19:0.138901,20:0.145684):0.072087,(21:0.118962,22:0.174237):0.094167):0.055314):0.114843):0.140145,(18:0.544702,(17:0.470016,((35:0.360506,((3:0.221408,(1:0.001594,2:0.003849):0.103813):0.060946,(7:0.32318,(6:0.15515,(4:0.095958,5:0.274962):0.07576):0.075985):0.040802):0.050598):0.080019,((11:0.188703,(8:0.270231,(9:0.085989,10:0.037257):0.176315):0.048397):0.041094,((12:0.240928,13:0.184008):0.137679,(16:0.305492,(14:0.192648,15:0.10231):0.123681):0.040588):0.056407):0.128727):0.126049):0.149538):0.116109):0.321754):0.3994105); 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 1362385953070; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 9012482431879006980; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 2376626579213555188; mqVersion 275; checksumv 0 3 3523983478 null getNumChars 365 numChars 365 getNumTaxa 35 numTaxa 35 short false bits 1048575 states 1048575 sumSquaresStatesOnly 1.94590114968217E14 sumSquares 1.94590114968217E14 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 -1280 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #9012482431879006980 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #9012482431879006980; 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 -1280 0; 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 #9012482431879006980 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 7305.1362361602004.351388881496134867; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -67; setLocation -1280 0; 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 #2376626579213555188 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -67; setLocation -1280 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; 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;