#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on September 19, 2025; 10:57 GMT TreeBASE (cc) 1994-2008 Study reference: Aguilera F., Mcdougall C., & Degnan B.M. 2013. Origin, evolution and classification of type-3 copper proteins: Lineage-specific gene expansions and losses across the Metazoa. BMC Evolutionary Biology, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S13985] [ The following blocks are input data for analysis step 11031 ] BEGIN TAXA; TITLE TaxaForAnalysisStep11031; DIMENSIONS NTAX=35; TAXLABELS Amphimedon_queenslandica_tyr Anopheles_gambiae_tyr1 Anopheles_gambiae_tyr2 Anopheles_gambiae_tyr3 Anopheles_gambiae_tyr4 Anopheles_gambiae_tyr5 Anopheles_gambiae_tyr6 Anopheles_gambiae_tyr7 Anopheles_gambiae_tyr8 Anopheles_gambiae_tyr9 Aspergillus_nidulans_tyr1 Aspergillus_nidulans_tyr2 Bombyx_mori_tyr1 Bombyx_mori_tyr2 Ciona_intestinalis_tyr1 Ciona_intestinalis_tyr2 Ciona_intestinalis_tyr3 'Ciona_intestinalis tyr4' Daphnia_pulex_tyr Dictyostelium_fasciculatum_tyr Drosophila_melanogaster_tyr1 Drosophila_melanogaster_tyr2 Drosophila_melanogaster_tyr3 Epiperipatus_sp_Hc Euphrynichus_bacillifer_HcA Euphrynichus_bacillifer_HcB Limulus_polyphemus_HcA Limulus_polyphemus_HcB Mastigoproctus_giganteus_HcA Mastigoproctus_giganteus_HcB Polysphondylium_pallidum_tyr2 Saccoglossus_kowaleksii_Hc Tribolium_castaneum_tyr1 Tribolium_castaneum_tyr2 Tribolium_castaneum_tyr3 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M16279] TITLE Beta_alignment_ML; LINK TAXA = TaxaForAnalysisStep11031; DIMENSIONS NCHAR=365; FORMAT DATATYPE=Protein SYMBOLS= "A C D E F G H I K L M N P Q R S T V W Y" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Amphimedon_queenslandica_tyr HSKEAQYLVAPSLKEHLFAMPAPTTADTLKAIETLSYWREDYDLNDHHYHWHLVYPWSHRTIDRQGELFLYMHSQMLARYNAERLSWSIGLVDPWSYDEVPSYTPPPGARPPLQGWLEEHSSKDTMIFWRNNINKGIIQGYFTKKENKFNLTMNWVGIIVEAEAHQIDSDYGTLHNLGHDKFGEINKNRWGVMGFTSVAVRDPVFWIWHRHIDDFRQSIVKKQHALKESAPPHVKLTGVQILPDGGIATYLTAPQLGLHNAKLNHEPYKWVVKVENLKPFTVRIFIAPKQMHEQRRYIEMDKFLCTLTTKSATFVRLDVESSVARKVPDEYQDPRCLCGWPQNMMIPNGTELGIDYVVFAILTND Anopheles_gambiae_tyr1 HRPDTKDLELPAFAQTFFIDSKKYTASDLDVEHRLWYFREDLGVNLHHWHWHLVYPIEIVDKDRRGELFYYMHQQIIARYNAERLSNHMARVQPFNLDEPEGYFPKMDAYPPRFDNTRLSDGIDDMKRWRERIYEAIHQGYVDTNNEKIVLDIDILGNIIEASDLTPNSTYGDFHNMGHILIAYSHLEYAGVMGDASTAMRDPIFYKWHAFIDNMFQEHKRLPYEKQELSFPDVRVESIQVEQVNRLTTFWQESDVDMSFTHLQHHEFSYTIKVEATRYGYVRIFLAPKLEQQRLMMVELDKFVVTMPPGSHTITRNSTESSVIPFERTELQNFLCGCGWPQHMLIPKGRPEGLRFELFVMVSND Anopheles_gambiae_tyr2 HRDDTRDVEIPSFLELFFVDPANYTASDRVDEQRVAYWREDIGLSLHHWHWHLVYPSTVVRKDRRGELFYHMHQQTIARYNIERFANGLARTLSFQLRESEAYFPKIVAFSCRYPNQVMKDRLADMDVSIKRIFEAIDNGYAATNGDRVPLDIDLIGDLLEASTNSINFNYGDYHQNGHVMLGYIYLEGVGVMGDLTTTMRDPLFYRWHQHIDDIFVRHKQRAYTSSELSFNDITVDSFDVQPKNVLLTFWQRSQFDLGFTHIQHAPFSYRIQATSMRRGTVRLFLGPKVRDQRRHMVELDKFTVNLRPGQNSIVRRSDESNLIPYERTMEVFQFCNCGWPSHMLLPKGSASGLEYDFFVMISND Anopheles_gambiae_tyr3 HRSDTSDVPVPSFLHLFFIDPANYTASDRVTEQRLAYFREDIGVNLHHWHWHLVYPAEVVRKDRRGELFYYMHQQMIARYQVERYSQGLGRVTPLNLRTPEPYYPKILTYPARYANMTLEDIISEVERQLQRIIAAIDEGVVAPSGQRTQLDIDILGNIVESSTISVNRQYGDTHNSGHVLLSLVFLESFGVMGDVTTAMRDPVFYRWHTFVDSIFQRHKQRPYGPAELRNPGVNLLSLETEVKNTLLTFWQRSQFDLGFTHLQHAAFNYRLQVATAKPATLRIFLAPKREEQRRLAIEMDTFRVNLTPGINNIIRRSANSSVIPYERTDANFRFCGCGWPSHMLVPKGDQFGVEYDLFAMLSDD Anopheles_gambiae_tyr4 HREDTKDVNIPSIVSLFFVDPANYTASDREDEQRMAYFREDIGVNMHHWHWHLVYPGDVVRKDRRGELFFYMHSQLIARYNADRFCAKLKKVRNLNYREPEGYYPKMISYPARAANTTLQDSVNDLERWRDRIHEAIDQGFVDKSGNRIMLDIDILGDVVEASSLTPNAQYGSLHNMGHNVIAYVYLEDYGVMGDVTTAMRDPIFYRWHGMIDGIFRRHKELPYTAEQLGNPGVTVNSVGVQPANVLLTYWQRSQVDLAFTHLQHAPFSFRVEVNAVRKGTLRIWLAPKSREQRRYFIEMDTSTVTLNPGMNTIVRRSDQSSVIPYERTLAQFRFCGCGWPQHMLVPKGSPEGVQFDLFAMVTDD Anopheles_gambiae_tyr5 HRPDTKDLNIPSFLELFFVDPSNYTASDREDEQRLAYFREDIGVNLHHWHWHLVYPGEVVNKDRRGELFYYMHQQLIARYNVERFCNRLARVRPLNLREPEGYFPKIIAFPPRPQNTVLRDTVSDLERSESRIAESIDGGYVGPGGNRIPLDIDVLGNIMEPSALSVNSQYGNYHGNLHNIIAYSFLEGYGVVGEFQTAMRDPSFYRLHAQVDNMFHRYKRTPYNANQLNYNGIQIQSLGVQPANVLLTYWQRSQVDLAFTHLQHAPFTFRLTVNATRRGTCRIFIGPKVDEQRLLMIELDKFTVNLNPGTNNIVRRSEQSSVIPYERTTEQFRFCNCGWPHHLLIPKGTPEGMQFDLFAMISND Anopheles_gambiae_tyr6 HRPDTKSVSVPSLLHLFFIDPANYTATDAEPEQRMAFFREDIGVNLHHWHWHLVYPASVVRKDRRGELFYYMHQQLLARYQIDRYAQGLGRIEPLNLREPEAYYPKLLTFCPRYPGMTISDRIADIESWLPRVLEAIDAGFASDDGVRVPLDIDVLGNILERSAISINRNYGDVHNMGHVLLAFIYLESSGVMGGVATAMRDPIFYRWHKFIDNIFLRNKARPYTMAELSNSNVTLEALETQAVNSFVTFWQRSQVDLRFTHLQCAPFVYRLRINSNRQDTVRIFLLPRQEDRRLLAIELDSFRVNLRPGMNNIVRQSSNSSVIPFERTNAQSRFCGCGWPAHMLLPKGNANGVEFDLFAMVSRD Anopheles_gambiae_tyr7 HRPDTKNLNIPSFFDLFFVDPTNYTASDREDEQRLAYFREDIGVNLHHWHWHLVYPGEVVNKDRRGELFYYMHQQLIARYNVDRFCNRLSRVRPLSLREPEGYFPKIVGFPARPQNTILRDSITDIELWGSRIAESIDGGYVAPGGNRIPLDIDVLGNIIEPSALSVNSQYGNYHGHMHNLISFSFLEGYGVVGEFQTAMRDPAFYRLHAQVDNMFHRYKRTPYNANQIGYAGVQIQSFGVQPANVLLTYWQRSQIDLGFTHLQHAPFTYRFAVNAARRGTCRIFIAPKTDEQRLLMIELDKFRVNLTPGVNNIVRRSEQSSVIPYERTTEQFRFCNCGWPHHLLLPKGTAEGMKFDLFLMISND Anopheles_gambiae_tyr8 HRTDTRDVEIPSFLELFYVDPANFTASDRVDEQRLAYWREDIGVNLHHWHWHLVYPARIVRKDRRGELFYYMHQQTMARYNIERFANGMPRVVAFNFREAEAYFPKITSYPARHPNETLSDSIADMELWTTRIFEAIDNGFASSSNQRVPLDIDLLGNIVEASTLSVNPQYGDLHNNGHNILGYIFLEGFGVVGDNTTAMRDPVFYRWHQHIDDIFVRHKQRAYTGQELAFNDVAVDSFEIQPVNILLTFWQRSQVNLGFTHIQHAPYSYRIRVNDTRRGTVRIFFGPKTREQRRLMVELDKFTVTLNAGANTIVRRSDQSSVIPYERTNEAFQFCNCGWPNHMLLPKGSPDGIEYDFFVMVSDD Anopheles_gambiae_tyr9 HRKDTGNVPVPSFLEMFFVDPASFSASEADPEQRLAYFREDIGVNLHHWHWHLVYPQEVVDKDRRGELFYYMHRQTVARYNVERFCNRLPAVKPLNLREPEAYFPKLLTYPGRHANMVLSHTILELESSLGRIKEAIQSGFAAADGTRVPLDIDILGNIMENSILSVNVPYGNYHSLGHVLIGFIYLEGHGVMGDFTTAMRDPTFYRFHGHVDDVFDMHKQKPYKAHELSFPGVSISDATVQARNRLLTFWQRTQVDLGFTHIQHAPFAYQIMVQEQKKGTVRIFLAPIYSQQRRYMLEMDKFVVKLHPGDNRIIRRSDQSSVIPYERTTESFRFCNCGWPDHMLLPKGHPDGQPFDLFIMISDD Aspergillus_nidulans_tyr1 HSKDAQQRFPPPLKNHPFFSTKICTADTLHGHALLSYWRDDYDLNDSHYYWHMVYRGAVGDFDRHGEVFLYVHSQMVARYETESLCWSLPLVRPWQYDDFNGYAPISSGYPPFSTWYSIRNPRARLEEWRDNIYAAIRKGQFTTSKDPLVLTLNFVGGILDAQYPSLDEEYGNLHNYGLGKFAEMEKSPYGLTISNFGAPRDPCFWRWYKHLQYYGRLAATRYPQDITAHRAEVVLSNLVVRLDGHITTFLGPPAVNFMKAKLGHEPYEWNVQVKNPQTLTLRLFIAAEDMNDYHSWIEMDRATVQLTDESATKVRLDTDSSVARKMGNRYASAVFRHGWPQNLMLPVGKVEGMPFVAFCIATDD Aspergillus_nidulans_tyr2 HSKDAQQRFPPPLKNHPFFSTKICTADTLHGHALLSYWRDDYDLNDSHYYWHMVYRGAVGDFDRHGEVFLYVHSQMVARYETESLCWSLPLVRPWQYDDFNGYAPISSGYPPFSTWYSIRNPRARLEEWRDNIYAAIRKGQFTTSKDPLVLTLNFVGGILDAQYPSLDEEYGNLHNYGLGKFAEMEKSPYGLTISNFGAPRDPCFWRWYKHLQYYGRLAATRYPQDITAHRAEVVLSNLVVRLDGHITTFLGPPAVNFMKAKLGHEPYEWNVQVKNPQTLTLRLFIAAEDMNDYHSWIEMDRATVQLTDESATKVRLDTDSSVARKMGNRYASAVFRHGWPQNLMLPVGKVEGMPFVAFCIATDD Bombyx_mori_tyr1 HRPDTKGLSIPTFAESFFMDPKNYTASDTEPEQRVAYFREDIGINLHHWHWHLVYPFDIVNKDRRGELFYYMHQQIIARYNVERMCNNLSRVRRYNFRAAEGYFPKLDAWPPRFAGTTIRDDVSELETWRDRFLQAIENMSVLPNGRQLPLDIDVLGNLMESSIISRNRPYGDLHNMGHVFISYSHLEQFGVMGDSATAMRDPVFYRWHAYIDDIFHLYKYKPYGNDRLDFPNIRVSSVSIETPNTLNTLWEQSTVDLGFTHLQHDEYNYVIEVNSSVMGMFRIFIAPTVDEQRKLMIELDKFSQGVKPGNNTIRRKSIDSSVIPYERTAAEFDFCGCGWPHHMLVPKGTTQGYPMVLFVMVSND Bombyx_mori_tyr2 HRRDTRKVRVKNFAEVFFLDSQDYTATDLEEEHRLAYWREDIGINLHHYHWHLVYPFTIVAKDRRGELFFYMHQQVIARFNCERLCNSLKRVKKFNWREPEAYFPKLDGWPPRQSGMQWQDTIDEMERWRRNVEEAIATGTVLPNGQTRPLDIDTLGNMLESSALSPNREYGSIHNNGHSFTAYMYLEQFGVIADEATTMRDPFFYRWHAYIDDVFQKHKESPYTRSELENPGVQVRSVSVEQPNTLNTFWMLSDVNLSFTHLNYRHFSYRINVNSSRRTTVRIFITPKFSDQRKMCIEMDRFVTVLNAGENNIVRQSTESSIIPFEQTLATFNYCGCGWPQHMLVPKGTEAGMPFQLFVMLSND Ciona_intestinalis_tyr1 HSKRAKSKQYPVPKPMDISNAAVTQRTGQPAETWMNYWRNDADLNYHHRHWHVVYVVGRPELFRQGELFGYMHAQMLARYNAERQSWRLPVVQAWQYNERVGYNTGFEGFSPRLPGSFPDREQTRFQRFERAIMRAINPPVVGETTRNVAMDANWAGHVIEASSSTWQAQLGSIHNNGHGVIGSMSRSGSSYMSATVTAMRDPIFYRWHKRIDNLWQEWSSRRVTDLQTDAPAVIIRPSDIIQSDDLQTYLGPPQKRYEDNKISHQPFTYHIRFQGELNLTVRIFICPASSNNRLSWIEMDKFVYRLGADATVISRPDRHSSVIKRERSTTATGFCECGWPYSMLLPRGTEQGEQWRLCVFLSDD Ciona_intestinalis_tyr2 HSKLCKKHRYPDPPKRDTQSAASGIGVGTPNELWMNYWRCDADFNFHHNHWHAVYRNGRNLKTRQGELFGYMHAQMLARFNADRETWGLEPVKAYEFDEVEGFDAGWEWIYPRPDKQIWPRIINENKHFEGEIEDLFDYGKIEYNGKEQPLNSNFVGHILESSSGRWQQQFGSFHNMGHMAFVYTGNRNTTYMGTPLCAVRDPIFFRWHQHVDDLYQMWNDKVLTNLTKNSPDVIIDPCDVMSCGEIKTKLREADLAFEDYKLDHEPFSYHIRLKGELRLTLRLFICQERVNKRRRWIEMDKFVYVMPANATVVKRQDRESSVIKRSHAEIKAGNCDCGWPYTMLLPRGNKNGEKWLLGVYVSDD Ciona_intestinalis_tyr3 HSKLCKKHRYPDPPKRDTQSAASGIGVGTPNELWMNYWRCDADFNFHHNHWHAVYRGGRNLKTRQGELFGYMHAQMLARFNADRETWGLEPVKAYEFDEVEGFDAGWEWIYPRPDKQIWPRIINENKHFEGEIEDLFDYGMIEYNGREQPLNSNFVGHILESSSGRWQRQFGGFHNMGHMAFVYTGNRNTTYMGTPLCAVRDPIFFRWHQHVDDLYQMWNDKVVTNLTKNSPDVIVDPCDVMSCGEIKTKLREADLAFEDYKLDHEPFSYHIRLKGELRLTLRLFICQERVNQRRRWIEMDKFVYVMPANATVVKRHDRESSVIKRSHAEIKAGNCDCGWPYTMLLPRGNKNGEKWLLGVYVSDD 'Ciona_intestinalis tyr4' HSKLCKKHRYPDPPKRDTQSAASGIGVGTPNELWMNYWRCDADFNFHHNHWHAVYRGGRNLKTRQGELFGYMHAQMLARFNADRETWGLEPVKAYEFDEVEGFDAGWEWIYPRPDKQIWPRIINENKHFEGEIEDLFDYGMIEYNGREQPLNSNFVGHILESSSGRWQRQFGGFHNMGHMAFVYTGNRNTTYMGTPLCAVRDPIFFRWHQHVDDLYQMWNDKVVTNLTKNSPDVIVDPCDVMSCGEIKTKLREADLAFEDYKLDHEPFSYHIRLKGELRLTLRLFICQERVNQRRRWIEMDKFVYVMPANATVVKRHDRESSVIKRSHAEIKAGNCDCGWPYTMLLPRGNKNGEKWLLGVYVSDD Daphnia_pulex_tyr QRQDSRSLRTPPIWEIFFFETRNFAATDRVVENKLSYFREDLGINSHHWHWHLIFPVEVNPPDRRGELFYYMHQQILARYDAERIANGLARVTSYDWDQPEAYFPKLTHWASRPSGLVLKDHIDDLQLWRTRILHAIHKGSVKGNGQVVHLDTNTLGELIEASQWSADKLYGDLHNFGHIAMCYIHSENMGVMGDSVTAMRDPIFYRWHKFIDSLFQQFKATPYSAQQLTLEGITVNSVEVHQKNLIITGWQESIVELDVTHLQHEDFSYRIQVTTSQDIVFRIFLAPIKREQRLLMIELDKFVARVTPGANLVKRKSDESSVIPFERTVKRTNFCGCGWPDHFLVPRGVPNGMPFTLFVMATSD Dictyostelium_fasciculatum_tyr HAPQFQSLQVPQALVIAVFCDQTIPKRWTNPDDLLKWWREDPMLNSHHWNWHTAYPSFAKLKDRQGELFVFMHRQMVARYDCERTALGIESLDPFTYKDSESFDPLLSTFVSRQSGSVMKDSLVDLEIWRQRLLEAIQKKTIASDGSMMTSEIADLGSSLEATMGSPNKAYGNLNKQAHNLMARVEQNNLGIMGDIIGAFRDPLFWRWHKHLDDFFHRFEIAPHKLEETAPPQFKVSKVSVKQENYLSTYMKSQIIDIKTYRLYHVPFNYEINVETFKKVVVRVYVVASDYGDRRKWVALDQFYTTLPEGQKTISRSSSESTILQRAVTTTLETYCKCGLPRNLLLPRGSKEGMKFKLCVVVTDD Drosophila_melanogaster_tyr1 HRKDTHDLDLPTIIEVFYVDSKDYTASDLDEEHRLWYFREDIGVNLHHWHWHLVYPFDIVDKDRRGELFYYMHQQLVARYNFERFSNRLQRVKRLNLREPEGYFPKLDAWPGRVDASVLKDDVADLERWIDRIYEAIHQGFVDESGNRIPLDIDHLGNIIESSILSPNRQYGDMHNMGHVFISYAHLESFGVMGDVATAMRDPVFYRWHSYIDDIFQEHKNKPYTRSQLTFDGISITGITVQPPNTFQTFWQQSDVDLSFTHLQHSPFVTTIMIEAQRMAFVRVFLAPKNRDQRLFMIELDKFLVALRPGANRIRRRSKESTVIPFERTEAEFNFCGCGWPAHMLIPKGLPEGLPADLFIMVSND Drosophila_melanogaster_tyr2 HRPDTQGLDLPSFSQTFFIDSQDYTASDLDPEHRLWYFREDLGINLHHWHWHLVYPFEIVAKDRRGELFYYMHQQVIARYNAERFSNNLARVLPFNLRDPEGYFPKMDAWPPRFESTRLSDEIGDLERWRDRIYEAIHQGFVDERGNRVPLDIDTLGNMIESSILSPNRVYGDLHNNGHTFISYAHLESFGVMGDVSTAMRDPVFYKWHSYIDRIFQEHKSRAYTENQLNYPGVSIAGIQVDRPNNLTTFWQQSDVDMSFTHLQHLPFTYTISLNAQRFGYVRIFMAPKNRDQRSMMIELDKFVTSLNPGPNTIRRRSTESSVIPFERTELEFNFCGCGWPNHMLVPKGLPEGLQCVLFIMVSND Drosophila_melanogaster_tyr3 HRPDTREVPITNISQIFFVEPSNYTASDREDEQRLAYFREDIGVNSHHWHWHLVYPTTVVNKDRRGELFYYMHHQILARYNVERFCNNLKKVQPLNLRVEEGYFPKILTYPARVTNQKLRDEISDVERWRDRVLAAIDQGYVDSSGNRIPLDIDILGNMIEASVLSINYNYGNLHNEGHNIISFAHLEEFGVMGDVTTAMRDPIFYRWHGFIDTVFNKFKTRPYNAGELNFDGITVDYIEAKKANTLLTYWQKSSADLAFTHLQNAPFTYTFNVTARRTGTCRIFICPKVEEQRLLAIEMDKFTVDLVPGENTIRRQSTESSVIPFERSLARFKFCGCGWPQHLLLPKGNAQGMVFDLFVMISDD Epiperipatus_sp_Hc QSPHTTNLLAPPIWQTMFFDQREPTGNNRDPEFKLSYFREDIAINSHHWHWHVIYPVGDKKINRKGELFYYMHEQMLARYDAERLCNGMRRVKSLDYDEIEGYYPRLHEYASRQANTRMMDTVIELERFRERIEHAISVGYILPDNTKTPLNIDILADLIEASNYSLNGAYGDLHNTGHVMLATAFNSSDGVMGFVQTALRDPLFYRWHKHIDNLLQNHKRTPYTDKELIADKIEIKEASITPKNKLYTFFDTKQLNLTITHLQHEEFTYNIKVNKDFTGTFRIFMAPKNNEQRILMIEMDKFQLKLSPGENNITRKSEDSNVLHKEMTPSSQHYCACGWPHHLLIPKGSAQGTAFHCFIMITDD Euphrynichus_bacillifer_HcA HRDDCRGVTVPPIQEVFFIPAEEQTGNILDSEYKVAYFREDIGINAHHWHWHIVYPTTHKVKDRKGELFYYMHQQMCARYDCERLSTELRRMIPFDFHQKEGYAPHLTNYASRPTGLSMSDDVQDMERWRERILDAIHGGFVDKEGNEVPLDLDMLGDLLESSYESVNREYGSLHNWGHVILAQVFKENPGVMSDTSTALRDPIFYRYHRFVDNIFQEYKISHYQKKDLDFPGVKVVNVTVNVPNVINTFLKESQLELSYHHLDHDPFTFSIGVEEVKNATVRVFLGPKYNEQRRFFIELDKFRATLEPGKTIITHKSSDSAVIDRTPTETNSEFCSCGWPQHMLIPRGNHRGMDFQLFVMLTDD Euphrynichus_bacillifer_HcB HRDDCKGVTVPPIQEIFFIPAEEETGNILDPEHTLAYYREDIGINAHHWHWHIAYPATGAVKDRKGELFFYMHQQMCARYDCERLSNGMNRMIPFNFEEHEGYAPHLTNYGSRPEGFSLRDDVQDMERWRERILESIHLGYVGHGEERIPLDTDILGAIIESSFESKNSTYGSLHNWGHVMMARMFQENPGVMSDTSTALRDPIFYRWHRFIDNIFQDYKATHYTKDDLSFDGIKVTDVVVKSDNVITTFMKEDELDLSYQHLDHEPFSISITVNAAKECIVRIFLAPQYEEGRRLFIELDKFKQTLAAGQSSFSRNAIDSNVLSKVPTDDYSEFCSCGWPENMLIPRGNHKGKPFVLFVLLTDD Limulus_polyphemus_HcA HRDDCKGLAVPPIQEIFFIPAEEETGNILNPEQRLAYFREDIEVNAHHWHWHLVFPATGKVKDRKGELFYYMHQQMCARYDCDRMSVGLQRMIPFNFEETEGYSAHLTHYASRPEGLHIRDSLQEMERWRERILEGINLGHVDDHGKEVELDIDILGALIESSHESKNEEYGSLHNWGHVMLARVFHENPGVMSDTSTSLRDPIFYRYHRFIDNMFQEYKASHYTKTELTFPEISISHVTIKVPNIIHTFMATDELELSYHHLNHEAFSYEIQVETVKHGTFRVFLAPKYNEQRRLFIELDKFHHGIHKGHNTIVRNSTESSVVSKIHTEKNTEYCSCGWPQHMLVPRGNEKGMDFQLFVMVTDD Limulus_polyphemus_HcB HRPDCKGVSLPPIQEIFFVTVQQTTGNILDPEYNLAYYREDIGINAHHWHWHLVYPATGKVKDRKGELFYYMHQQMCARYDCERLSNGMPRMEPFNFHEPEGYSSHLSPYPSRPDGMTLQDSVQDLERWRDRISDAIHIGHVDENGSHVPLDIDILGAMVEASYESINQAYGSIHNWGHVISARVYHLNPGVMSDTATSLRDPIFYRWHRFIDNMFQDYKETHYNHSDLEFPGIEITKVLLNHTNNINTFKEFSVLDLSFSHLNHEDFHYKIQVEKTKPATVRIFMAPKYKNLRRLMIEMDKFHAEIHPGHNTIVRHSKDSSVISSARSEHANEYCSCGWPDHLLVPRGDEKGMPFHLFVMLTDD Mastigoproctus_giganteus_HcA HRSDCDGIIVPPIQEIFFIPAEQETGNIFDPEYHLAYFREDIGANAHHWHWHIVYPGTHITKDRKGELFYYMHQQMCARYDCDRLSTGLRRLIPFNFHEEEGYNPHLTNYASRPAGLSMKDDVQDMIRWRERILDAIHIGFLDDHGNEIPLDTDLLADLMESSYESKNREYGSLHNWGHVIISQCFKENPGVMSDTSTSLRDPIFYRYHRFVDNIFQELKASPYKQSELDFTGIDVVNVTVNAPNLVHTFFAEDQLELRYHHLDHEPFTYNISVEAEKDSTVRIFLGPKYDEARRFYIELDKFHAKLSPGKNVVTRKSSESNVANKTPNASSDQFCSCGWPNYMLLPRGNHKGMEFELFVMLTDD Mastigoproctus_giganteus_HcB HRDDCKGVHIPPIQEIFFIPAEEKTGNILDPEYKLAYYREDIETNAHHWHWHIVYPATGHIKDRKGELFYYMHQQMCARYDCERLSNGMNRMIPFNFEEKEGYAPHLIQYGARPQGFSLRDDVQSMERWRERIIEAIQLGYVDEHGEHVNLDADIIGALIESSHDSKNSRYGSLHNWGHVMMARMYQENPGVMSDTSTSLRDPIFYRWHRFVDNIFKDYKSTPYEKEEYSFDGIEVLEVTVKTDNVLTTFLKEDILELTYDHLDHEPFHYSIDVQATKEATVRIFLGPKYEDKRRLMIELDKFHKTLAPGKNTISRNSVDSSVVSHVPTANNQEYCSCGWPGHMLIPRGTRKGMDFHLYVVLTDD Polysphondylium_pallidum_tyr2 HSPHFQVLQVPQALVIAVFVDKNIPKRWRNPDALLKWWREDPMLNSHHWNWHTAYPSFAKLKDRQGELFVFMHRQMVARYDCERTALGLQPIDQFSYRESDAFDPLISMFVPRPADSKMRDSIVDLEIWRERLFEAIQKKSVQQDGTVTTTEIADLGSSLEATMGSPNKSYGNLNKQAHNLMSRVEQTSIGIMGDIIGAFRDPMFWRWHKHLDEFFHRFELTPYNIVDYAPANIRIANAVVRPENNLYTYMKTQIIAIKTNRLYYVPFNYEISVLKYKKVVVRVYIVASDYGDRRKWISLDQFFTALPEGQKTITRSSSESTILQQAATPSTETYCKCGLPRNLLLPRGTKEGMPFKIAVIVTDD Saccoglossus_kowaleksii_Hc HHSLARSNKVPEFTDAPDMSTHMVPPVGEPEEIWMDYWRHDADFVDHHRHWHRVYRARADHLDRQGELFVYMHRQMLARYNAEREAWGLEPVEPWEFTDVLGSDAGDEGIRPRPAGLKWSMDIRQFQVWTNNIRRAFRENIIPNQGAQSALQANWVGHIVEATSGTFYDNYGSLHNSGHGVFGQLQSGFSTYMATTAHAVRDHIFFRWHKFIDNLVEEYHQTQKTELGVDSPPVVIEENDIISSDLIETTLDLPQRQFEWGKLSHNAFNYHLRIRQELRLTFRIFICPAQANDRRRWIEMDKFRYILGAMETIITRQDVHSSVIRRFPQRTVSGFCECGWPYNLLLPRGKADGEKYLIAVLISDD Tribolium_castaneum_tyr1 HRPDTQNLDLPSFIHVFYVDSQDFTASDLDEEHRVAYWREDIGLNLHHWHWHLVYPFEIVDKNRRGEIFYYMHQQIIARFNIERLCNGLKRVVKLNWREPEAYFPKLDTWPARPVNQVPRDSLDDMDRWRDRIYDAIHSGVVGDNGQNIPLTIDVLGNIIESSILSPNRNYGDFHNMGHILIGYIFLEPFGVMADPAVDLRDPLFFRWHAYIDDMFQEFKATRYTVAQLNYPGVTVTNIEVQKPNVLSTFWQQSDLDLSFTHLQNQDFTYKITVNNNRMGTCRIFLAPQFRNQKDMFIELDRFAVSLKQGTNTITRHSTESSLIPFERTLSEFNFCGCGWPQHMLLPKGTEAGYPCHLFVMISND Tribolium_castaneum_tyr2 HRQDTQDIDLPSFIESFYVDSKDYTASDLEEEHRLAYFREDLGINLHHWHWHLVYPFEVVAKNRRGELFYYMHQQIIARYNFERLCNKLKRATRFDFNEAEAYFPKLDAWPSRVANQKLRDDVEDLKRWSDRIYAAIHQGSVDERGRSITLTIDILGNMIESSILSPNRTYGDLHNMGHVFISYIHLESFGVMGDSATAMRDPIFYRWHSYIDDIFQEYKATRYTENQLNYPGITVSNIEVQSKNTFNTFWQQSDVDLSFTHLQHQPFTYKITVNGNRKGTCRIFLAPKTRDQKIMFIELDKFTVNLKQGQNTITRASSQSSVIPFERTLAQFNFCGCGWPQHMLIPKGTPEGMKSQLFVMISND Tribolium_castaneum_tyr3 HRQDTQDIDLPSFIESFYVDSKDYTASDLEEEHRLAYFREDLGINLHHWHWHLVYPFEVVAKNRRGELFYYMHQQIIARYNFERLCNKLKRATRFDFNEAEAYFPKLDAWPSRVANQKLRDDVEDLKRWSDRIYAAIHQGSVDERGRSITLTIDILGNMIESSILSPNRTYGDLHNMGHVFISYIHLESFGVMGDSATAMRDPIFYRWHSYIDDIFQEYKATRYTENQLNYPGITVSNIEVPSKNTFNTFWQQSDVDLSFTHLQHQPFTYKITVNGNRKGTCRIFLAPKTRDQKIMFIELDKFTVNLKQGQNTITRASSQSSVIPFERTLAQFNFCGCGWPQHMLIPKGTPEGMKSQLFVMISND ; END; [ The following blocks are output data for analysis step 11031 ] BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_19 = [&R] (((((((((((((Anopheles_gambiae_tyr7:0.089539,Anopheles_gambiae_tyr5:0.034345):0.222488,((Anopheles_gambiae_tyr2:0.194847,Anopheles_gambiae_tyr8:0.167425):0.134572,Anopheles_gambiae_tyr9:0.462837):0.06622):0.096941,(Anopheles_gambiae_tyr3:0.302446,Anopheles_gambiae_tyr6:0.224945):0.251903):0.045701,Anopheles_gambiae_tyr4:0.265268):0.067276,Drosophila_melanogaster_tyr3:0.403684):0.091009,(((Drosophila_melanogaster_tyr2:0.102097,Anopheles_gambiae_tyr1:0.388621):0.107518,Drosophila_melanogaster_tyr1:0.147887):0.09612,((Bombyx_mori_tyr1:0.369535,Bombyx_mori_tyr2:0.559434):0.066279,((Tribolium_castaneum_tyr3:0.00257,Tribolium_castaneum_tyr2:0.0):0.14696,Tribolium_castaneum_tyr1:0.269112):0.056257):0.062202):0.105668):0.210595,Daphnia_pulex_tyr:0.798):0.176305,(Limulus_polyphemus_HcB:0.347648,((Euphrynichus_bacillifer_HcB:0.166108,Mastigoproctus_giganteus_HcB:0.187199):0.067784,(Limulus_polyphemus_HcA:0.26402,(Mastigoproctus_giganteus_HcA:0.259293,Euphrynichus_bacillifer_HcA:0.150671):0.108957):0.073027):0.142585):0.300572):0.170034,Epiperipatus_sp_Hc:0.548526):0.25833,(Dictyostelium_fasciculatum_tyr:0.231167,Polysphondylium_pallidum_tyr2:0.095495):0.978666):0.44895,(Ciona_intestinalis_tyr1:0.467071,(((Ciona_intestinalis_tyr3:0.0,'Ciona_intestinalis tyr4':0.0):0.017849,Ciona_intestinalis_tyr2:0.013588):0.76666,Saccoglossus_kowaleksii_Hc:0.796161):0.097888):0.911534):0.602855,Amphimedon_queenslandica_tyr:0.638001):1.342018,Aspergillus_nidulans_tyr1:0.0,Aspergillus_nidulans_tyr2:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61747] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_26 = [&R] (((((((((((((Anopheles_gambiae_tyr8:0.130619,Anopheles_gambiae_tyr2:0.309519):0.164987,Anopheles_gambiae_tyr9:0.389164):0.078612,(Anopheles_gambiae_tyr6:0.316382,Anopheles_gambiae_tyr3:0.233485):0.109784):0.12399,((Anopheles_gambiae_tyr5:0.062906,Anopheles_gambiae_tyr7:0.087733):0.326365,Anopheles_gambiae_tyr4:0.249051):0.051895):0.021023,Drosophila_melanogaster_tyr3:0.279585):0.108675,((((Anopheles_gambiae_tyr1:0.325635,Drosophila_melanogaster_tyr2:0.099257):0.105858,Drosophila_melanogaster_tyr1:0.206207):0.110204,((Tribolium_castaneum_tyr2:0.0,Tribolium_castaneum_tyr3:0.002954):0.114689,Tribolium_castaneum_tyr1:0.304694):0.064351):0.099562,(Bombyx_mori_tyr2:0.583434,Bombyx_mori_tyr1:0.360406):0.083007):0.132523):0.146924,Daphnia_pulex_tyr:0.663492):0.265969,(Limulus_polyphemus_HcB:0.235692,((Euphrynichus_bacillifer_HcA:0.134721,Mastigoproctus_giganteus_HcA:0.219657):0.135345,((Mastigoproctus_giganteus_HcB:0.215514,Limulus_polyphemus_HcA:0.295272):0.017611,Euphrynichus_bacillifer_HcB:0.181858):0.050066):0.168344):0.22239):0.168815,Epiperipatus_sp_Hc:0.811419):0.258982,(Dictyostelium_fasciculatum_tyr:0.18896,Polysphondylium_pallidum_tyr2:0.119193):1.199243):0.499394,((Ciona_intestinalis_tyr1:0.825563,(Ciona_intestinalis_tyr2:0.014225,(Ciona_intestinalis_tyr3:0.0,'Ciona_intestinalis tyr4':0.0):0.007432):0.715322):0.307573,Saccoglossus_kowaleksii_Hc:0.726114):0.758569):0.614292,Amphimedon_queenslandica_tyr:0.782999):1.135537,Aspergillus_nidulans_tyr2:0.0,Aspergillus_nidulans_tyr1:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61754] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE ML_tree = [&R] ((Dictyostelium_fasciculatum_tyr:0.182039,Polysphondylium_pallidum_tyr2:0.150843):0.5830955,(((Amphimedon_queenslandica_tyr:0.678779,(Aspergillus_nidulans_tyr2:0.0,Aspergillus_nidulans_tyr1:0.0):1.141386):0.616772,(Saccoglossus_kowaleksii_Hc:0.599874,(Ciona_intestinalis_tyr1:0.588569,(Ciona_intestinalis_tyr2:0.01461,('Ciona_intestinalis tyr4':0.0,Ciona_intestinalis_tyr3:0.0):0.013786):0.815026):0.259864):0.96334):0.485477,((Limulus_polyphemus_HcB:0.25913,(Limulus_polyphemus_HcA:0.21149,((Euphrynichus_bacillifer_HcB:0.18517,Mastigoproctus_giganteus_HcB:0.193561):0.092517,(Euphrynichus_bacillifer_HcA:0.155567,Mastigoproctus_giganteus_HcA:0.233827):0.120013):0.07575):0.14703):0.17733,(Epiperipatus_sp_Hc:0.755677,(Daphnia_pulex_tyr:0.650614,(((Bombyx_mori_tyr1:0.401314,Bombyx_mori_tyr2:0.498944):0.071384,((Tribolium_castaneum_tyr1:0.298118,(Tribolium_castaneum_tyr2:0.0,Tribolium_castaneum_tyr3:0.002871):0.121853):0.076398,(Drosophila_melanogaster_tyr1:0.212909,(Drosophila_melanogaster_tyr2:0.123086,Anopheles_gambiae_tyr1:0.353335):0.100135):0.112501):0.046755):0.093413,(Drosophila_melanogaster_tyr3:0.339754,((Anopheles_gambiae_tyr7:0.112917,Anopheles_gambiae_tyr5:0.042059):0.242547,(Anopheles_gambiae_tyr4:0.251395,((Anopheles_gambiae_tyr6:0.331563,Anopheles_gambiae_tyr3:0.238441):0.175199,(Anopheles_gambiae_tyr9:0.418831,(Anopheles_gambiae_tyr2:0.267953,Anopheles_gambiae_tyr8:0.123428):0.158982):0.064126):0.106186):0.035698):0.069371):0.153917):0.206214):0.21597):0.16878):0.465743):0.5830955); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61728] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_20 = [&R] ((((((((((((((Tribolium_castaneum_tyr2:0.0,Tribolium_castaneum_tyr3:0.005648):0.150155,Tribolium_castaneum_tyr1:0.257712):0.087078,(Drosophila_melanogaster_tyr1:0.185263,Drosophila_melanogaster_tyr2:0.17817):0.070741):0.089768,Bombyx_mori_tyr1:0.454643):0.05668,Bombyx_mori_tyr2:0.453022):0.048884,(((((Anopheles_gambiae_tyr5:0.02798,Anopheles_gambiae_tyr7:0.108149):0.175312,Anopheles_gambiae_tyr4:0.283895):0.081108,((Anopheles_gambiae_tyr8:0.1124,Anopheles_gambiae_tyr2:0.214765):0.206044,Anopheles_gambiae_tyr9:0.373224):0.108411):0.041626,(Anopheles_gambiae_tyr3:0.217222,Anopheles_gambiae_tyr6:0.365882):0.250945):0.17154,Drosophila_melanogaster_tyr3:0.333729):0.229091):0.10345,Anopheles_gambiae_tyr1:0.283512):0.282637,Daphnia_pulex_tyr:0.692513):0.19908,Epiperipatus_sp_Hc:0.714447):0.252988,(Limulus_polyphemus_HcB:0.367781,(((Euphrynichus_bacillifer_HcA:0.156641,Mastigoproctus_giganteus_HcA:0.234978):0.148579,Limulus_polyphemus_HcA:0.237439):0.07011,(Mastigoproctus_giganteus_HcB:0.187673,Euphrynichus_bacillifer_HcB:0.169775):0.054988):0.09377):0.243228):0.846395,(Polysphondylium_pallidum_tyr2:0.145063,Dictyostelium_fasciculatum_tyr:0.179111):1.383857):0.411087,(((('Ciona_intestinalis tyr4':0.0,Ciona_intestinalis_tyr3:0.0):0.006662,Ciona_intestinalis_tyr2:0.014274):0.957444,Ciona_intestinalis_tyr1:0.588433):0.334214,Saccoglossus_kowaleksii_Hc:0.683805):0.881347):0.59762,Amphimedon_queenslandica_tyr:0.602294):1.182452,Aspergillus_nidulans_tyr1:0.0,Aspergillus_nidulans_tyr2:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61748] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_10 = [&R] (((((((((((Anopheles_gambiae_tyr6:0.312548,Anopheles_gambiae_tyr3:0.213107):0.1898,Anopheles_gambiae_tyr4:0.183177):0.045416,((Anopheles_gambiae_tyr8:0.107723,Anopheles_gambiae_tyr2:0.255994):0.201614,(Anopheles_gambiae_tyr9:0.390501,(Anopheles_gambiae_tyr5:0.023457,Anopheles_gambiae_tyr7:0.092899):0.212459):0.091507):0.035107):0.072657,(((((Bombyx_mori_tyr2:0.422173,Tribolium_castaneum_tyr1:0.183127):0.111657,(Tribolium_castaneum_tyr2:0.0,Tribolium_castaneum_tyr3:0.002705):0.150229):0.07367,((Drosophila_melanogaster_tyr2:0.085651,Anopheles_gambiae_tyr1:0.326746):0.076143,Drosophila_melanogaster_tyr1:0.181982):0.106488):0.073991,Bombyx_mori_tyr1:0.328692):0.126377,Drosophila_melanogaster_tyr3:0.349138):0.049916):0.199386,Daphnia_pulex_tyr:0.654169):0.198564,Epiperipatus_sp_Hc:0.715143):0.203651,((((Euphrynichus_bacillifer_HcA:0.128173,Mastigoproctus_giganteus_HcA:0.248034):0.151132,Limulus_polyphemus_HcA:0.207758):0.066181,(Euphrynichus_bacillifer_HcB:0.199032,Mastigoproctus_giganteus_HcB:0.208021):0.057078):0.208652,Limulus_polyphemus_HcB:0.199239):0.246768):0.417013,(Polysphondylium_pallidum_tyr2:0.127912,Dictyostelium_fasciculatum_tyr:0.183213):1.08786):0.376,(Saccoglossus_kowaleksii_Hc:0.650524,(((Ciona_intestinalis_tyr3:0.0,'Ciona_intestinalis tyr4':0.0):0.026211,Ciona_intestinalis_tyr2:6.0E-6):0.801957,Ciona_intestinalis_tyr1:0.584144):0.255862):0.678745):0.59411,Amphimedon_queenslandica_tyr:0.6532):1.174067,Aspergillus_nidulans_tyr1:0.0,Aspergillus_nidulans_tyr2:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61738] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_15 = [&R] ((((((((((((Anopheles_gambiae_tyr2:0.270529,Anopheles_gambiae_tyr8:0.103244):0.156199,Anopheles_gambiae_tyr9:0.390832):0.036892,(Anopheles_gambiae_tyr3:0.172105,Anopheles_gambiae_tyr6:0.33094):0.194236):0.079696,(Drosophila_melanogaster_tyr3:0.322917,(Anopheles_gambiae_tyr4:0.194126,(Anopheles_gambiae_tyr5:0.047375,Anopheles_gambiae_tyr7:0.107332):0.18487):0.044711):0.044636):0.149495,(((((Tribolium_castaneum_tyr3:0.002759,Tribolium_castaneum_tyr2:0.0):0.103156,Tribolium_castaneum_tyr1:0.285218):0.042473,((Drosophila_melanogaster_tyr2:0.070819,Anopheles_gambiae_tyr1:0.285794):0.075583,Drosophila_melanogaster_tyr1:0.196203):0.147692):0.080435,Bombyx_mori_tyr1:0.416146):0.035116,Bombyx_mori_tyr2:0.423588):0.077398):0.176192,Daphnia_pulex_tyr:0.4389):0.27486,((((Euphrynichus_bacillifer_HcA:0.149852,Mastigoproctus_giganteus_HcA:0.181617):0.10563,(Mastigoproctus_giganteus_HcB:0.164203,Euphrynichus_bacillifer_HcB:0.145122):0.096623):0.10081,Limulus_polyphemus_HcA:0.171917):0.163846,Limulus_polyphemus_HcB:0.265256):0.233652):0.107112,Epiperipatus_sp_Hc:0.528058):0.432018,(Dictyostelium_fasciculatum_tyr:0.232847,Polysphondylium_pallidum_tyr2:0.024551):1.239799):0.329129,(((('Ciona_intestinalis tyr4':0.0,Ciona_intestinalis_tyr3:0.0):0.02812,Ciona_intestinalis_tyr2:0.008968):0.668917,Ciona_intestinalis_tyr1:0.494049):0.296158,Saccoglossus_kowaleksii_Hc:0.461981):0.977711):0.613956,Amphimedon_queenslandica_tyr:0.816124):0.842377,Aspergillus_nidulans_tyr2:0.0,Aspergillus_nidulans_tyr1:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61743] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_11 = [&R] ((((((((((((Anopheles_gambiae_tyr5:0.032343,Anopheles_gambiae_tyr7:0.105444):0.177306,(((Anopheles_gambiae_tyr8:0.140834,Anopheles_gambiae_tyr2:0.234953):0.200098,(Anopheles_gambiae_tyr6:0.274799,Anopheles_gambiae_tyr3:0.256434):0.164983):0.068714,Anopheles_gambiae_tyr9:0.409683):0.053082):0.103914,Drosophila_melanogaster_tyr3:0.369261):0.044457,Anopheles_gambiae_tyr4:0.161803):0.095588,((Bombyx_mori_tyr2:0.420495,Bombyx_mori_tyr1:0.420064):0.075909,(((Tribolium_castaneum_tyr3:0.002722,Tribolium_castaneum_tyr2:0.0):0.061196,Tribolium_castaneum_tyr1:0.262157):0.058273,(Drosophila_melanogaster_tyr1:0.158355,(Anopheles_gambiae_tyr1:0.296734,Drosophila_melanogaster_tyr2:0.127033):0.069083):0.173175):0.060753):0.093635):0.202385,Daphnia_pulex_tyr:0.642458):0.15151,Epiperipatus_sp_Hc:0.953997):0.188698,((((Mastigoproctus_giganteus_HcA:0.176003,Euphrynichus_bacillifer_HcA:0.13554):0.167679,Limulus_polyphemus_HcA:0.225566):0.048127,(Mastigoproctus_giganteus_HcB:0.156639,Euphrynichus_bacillifer_HcB:0.178698):0.080357):0.203383,Limulus_polyphemus_HcB:0.307478):0.195488):0.288483,(Dictyostelium_fasciculatum_tyr:0.169269,Polysphondylium_pallidum_tyr2:0.151603):0.863632):0.422483,(((('Ciona_intestinalis tyr4':0.0,Ciona_intestinalis_tyr3:0.0):0.017263,Ciona_intestinalis_tyr2:1.0E-6):0.80044,Ciona_intestinalis_tyr1:0.506641):0.224562,Saccoglossus_kowaleksii_Hc:0.590869):1.031451):0.584674,Amphimedon_queenslandica_tyr:0.577267):1.052866,Aspergillus_nidulans_tyr2:0.0,Aspergillus_nidulans_tyr1:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61739] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_5 = [&R] ((((((((((((Anopheles_gambiae_tyr9:0.406419,((Anopheles_gambiae_tyr3:0.21039,Anopheles_gambiae_tyr6:0.325171):0.157016,(Anopheles_gambiae_tyr8:0.131791,Anopheles_gambiae_tyr2:0.254229):0.123992):0.061376):0.060716,(Anopheles_gambiae_tyr5:0.04255,Anopheles_gambiae_tyr7:0.097372):0.182092):0.050235,Anopheles_gambiae_tyr4:0.281698):0.061264,Drosophila_melanogaster_tyr3:0.33577):0.136281,((((Anopheles_gambiae_tyr1:0.306536,Drosophila_melanogaster_tyr2:0.120965):0.092654,Drosophila_melanogaster_tyr1:0.182987):0.136244,((Tribolium_castaneum_tyr3:0.002862,Tribolium_castaneum_tyr2:0.0):0.131147,Tribolium_castaneum_tyr1:0.285208):0.015605):0.09415,(Bombyx_mori_tyr2:0.377329,Bombyx_mori_tyr1:0.441487):0.051499):0.115292):0.141862,Daphnia_pulex_tyr:0.695083):0.310217,((Limulus_polyphemus_HcA:0.188796,((Euphrynichus_bacillifer_HcB:0.188711,Mastigoproctus_giganteus_HcB:0.187038):0.064846,(Mastigoproctus_giganteus_HcA:0.221569,Euphrynichus_bacillifer_HcA:0.220119):0.130091):0.062098):0.155691,Limulus_polyphemus_HcB:0.190604):0.356893):0.124057,Epiperipatus_sp_Hc:0.600134):0.296886,(Polysphondylium_pallidum_tyr2:0.068346,Dictyostelium_fasciculatum_tyr:0.244751):1.375383):0.497207,((((Ciona_intestinalis_tyr3:0.0,'Ciona_intestinalis tyr4':0.0):0.005571,Ciona_intestinalis_tyr2:0.00369):0.698405,Saccoglossus_kowaleksii_Hc:0.658937):0.370019,Ciona_intestinalis_tyr1:0.474448):1.098244):0.854842,Amphimedon_queenslandica_tyr:0.678504):0.993888,Aspergillus_nidulans_tyr1:0.0,Aspergillus_nidulans_tyr2:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61733] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_16 = [&R] (((((((((((Drosophila_melanogaster_tyr1:0.193702,(Drosophila_melanogaster_tyr2:0.089893,Anopheles_gambiae_tyr1:0.339667):0.093054):0.053299,((Tribolium_castaneum_tyr2:0.0,Tribolium_castaneum_tyr3:0.0):0.128368,(Tribolium_castaneum_tyr1:0.230153,Bombyx_mori_tyr2:0.518048):0.042248):0.118077):0.066311,Bombyx_mori_tyr1:0.356723):0.141003,(Drosophila_melanogaster_tyr3:0.322291,(((((Anopheles_gambiae_tyr2:0.228462,Anopheles_gambiae_tyr8:0.119753):0.159117,(Anopheles_gambiae_tyr6:0.304952,Anopheles_gambiae_tyr3:0.15922):0.173837):0.091872,Anopheles_gambiae_tyr9:0.425751):0.052776,(Anopheles_gambiae_tyr5:0.027318,Anopheles_gambiae_tyr7:0.089714):0.184365):0.061105,Anopheles_gambiae_tyr4:0.324817):0.086732):0.112989):0.175688,Daphnia_pulex_tyr:0.488808):0.177774,Epiperipatus_sp_Hc:0.574515):0.178295,((((Mastigoproctus_giganteus_HcA:0.221467,Euphrynichus_bacillifer_HcA:0.149404):0.071388,(Euphrynichus_bacillifer_HcB:0.18298,Mastigoproctus_giganteus_HcB:0.13902):0.075755):0.08637,Limulus_polyphemus_HcA:0.14844):0.177611,Limulus_polyphemus_HcB:0.202949):0.11819):0.355449,(Dictyostelium_fasciculatum_tyr:0.236675,Polysphondylium_pallidum_tyr2:0.132754):1.005883):0.488228,((Ciona_intestinalis_tyr1:0.428494,(('Ciona_intestinalis tyr4':0.0,Ciona_intestinalis_tyr3:0.0):0.023707,Ciona_intestinalis_tyr2:0.006712):0.604754):0.201124,Saccoglossus_kowaleksii_Hc:0.537794):0.838556):0.534238,Amphimedon_queenslandica_tyr:0.586023):1.027546,Aspergillus_nidulans_tyr2:0.0,Aspergillus_nidulans_tyr1:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61744] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_4 = [&R] (((((((((((((Anopheles_gambiae_tyr8:0.12895,Anopheles_gambiae_tyr2:0.235941):0.16207,Anopheles_gambiae_tyr9:0.410137):0.062461,(Anopheles_gambiae_tyr3:0.283969,Anopheles_gambiae_tyr6:0.323811):0.178283):0.048398,Drosophila_melanogaster_tyr3:0.32575):0.05543,((Anopheles_gambiae_tyr7:0.154024,Anopheles_gambiae_tyr5:0.016967):0.233572,Anopheles_gambiae_tyr4:0.203702):0.052127):0.17893,(((Bombyx_mori_tyr2:0.557672,Bombyx_mori_tyr1:0.304116):0.113249,(Tribolium_castaneum_tyr1:0.317986,(Tribolium_castaneum_tyr3:0.002726,Tribolium_castaneum_tyr2:0.0):0.101799):0.050522):0.06162,((Drosophila_melanogaster_tyr2:0.145796,Anopheles_gambiae_tyr1:0.381133):0.124223,Drosophila_melanogaster_tyr1:0.18943):0.045878):0.157625):0.236617,Daphnia_pulex_tyr:0.710415):0.298869,(Limulus_polyphemus_HcB:0.227694,(((Mastigoproctus_giganteus_HcA:0.269627,Euphrynichus_bacillifer_HcA:0.141488):0.081914,Limulus_polyphemus_HcA:0.269969):0.068357,(Euphrynichus_bacillifer_HcB:0.206958,Mastigoproctus_giganteus_HcB:0.227985):0.062638):0.2339):0.195339):0.24963,Epiperipatus_sp_Hc:0.674264):0.243439,(Dictyostelium_fasciculatum_tyr:0.203331,Polysphondylium_pallidum_tyr2:0.121977):1.033201):0.885667,(Saccoglossus_kowaleksii_Hc:0.723931,((('Ciona_intestinalis tyr4':0.0,Ciona_intestinalis_tyr3:0.0):0.006604,Ciona_intestinalis_tyr2:0.016411):0.973516,Ciona_intestinalis_tyr1:0.684048):0.233016):1.021316):0.717314,Amphimedon_queenslandica_tyr:0.852904):1.528717,Aspergillus_nidulans_tyr1:0.0,Aspergillus_nidulans_tyr2:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61732] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_13 = [&R] (((((((((((Anopheles_gambiae_tyr4:0.235009,((Anopheles_gambiae_tyr9:0.441897,(Anopheles_gambiae_tyr2:0.291473,Anopheles_gambiae_tyr8:0.081843):0.135424):0.062862,(Anopheles_gambiae_tyr3:0.252397,Anopheles_gambiae_tyr6:0.243839):0.129403):0.071066):0.053524,(Anopheles_gambiae_tyr7:0.118921,Anopheles_gambiae_tyr5:0.037658):0.288877):0.046447,Drosophila_melanogaster_tyr3:0.342217):0.155344,(Bombyx_mori_tyr1:0.401601,(((Bombyx_mori_tyr2:0.447209,Tribolium_castaneum_tyr1:0.202576):0.081427,(Tribolium_castaneum_tyr2:0.0,Tribolium_castaneum_tyr3:0.0):0.161929):0.059874,((Drosophila_melanogaster_tyr2:0.139219,Anopheles_gambiae_tyr1:0.329642):0.080379,Drosophila_melanogaster_tyr1:0.220707):0.08359):0.078962):0.051434):0.194938,Daphnia_pulex_tyr:0.597231):0.234268,Epiperipatus_sp_Hc:0.806947):0.150119,((((Euphrynichus_bacillifer_HcA:0.156537,Mastigoproctus_giganteus_HcA:0.249947):0.121337,(Mastigoproctus_giganteus_HcB:0.146993,Euphrynichus_bacillifer_HcB:0.167615):0.113791):0.054792,Limulus_polyphemus_HcA:0.167939):0.12457,Limulus_polyphemus_HcB:0.225831):0.233596):0.396705,(Polysphondylium_pallidum_tyr2:0.137377,Dictyostelium_fasciculatum_tyr:0.13852):1.080476):0.364704,(Saccoglossus_kowaleksii_Hc:0.651955,(((Ciona_intestinalis_tyr3:0.0,'Ciona_intestinalis tyr4':0.0):1.0E-6,Ciona_intestinalis_tyr2:0.035763):0.847552,Ciona_intestinalis_tyr1:0.429696):0.286545):1.289761):0.460551,Amphimedon_queenslandica_tyr:0.559545):0.960812,Aspergillus_nidulans_tyr1:0.0,Aspergillus_nidulans_tyr2:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61741] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_8 = [&R] ((((((((((((Anopheles_gambiae_tyr3:0.235445,Anopheles_gambiae_tyr6:0.352225):0.148182,Anopheles_gambiae_tyr4:0.23569):0.051105,((Anopheles_gambiae_tyr8:0.085477,Anopheles_gambiae_tyr2:0.346805):0.156747,((Anopheles_gambiae_tyr5:0.058333,Anopheles_gambiae_tyr7:0.109404):0.206556,Anopheles_gambiae_tyr9:0.319018):0.06698):0.025538):0.0749,Drosophila_melanogaster_tyr3:0.362822):0.077455,((((Tribolium_castaneum_tyr1:0.288125,Bombyx_mori_tyr2:0.350978):0.088054,(Tribolium_castaneum_tyr3:0.0,Tribolium_castaneum_tyr2:0.0):0.156516):0.033684,Bombyx_mori_tyr1:0.410267):0.045896,((Drosophila_melanogaster_tyr2:0.056834,Anopheles_gambiae_tyr1:0.366079):0.085642,Drosophila_melanogaster_tyr1:0.24305):0.056718):0.15426):0.219595,Daphnia_pulex_tyr:0.545873):0.159364,Epiperipatus_sp_Hc:0.71243):0.24872,(Limulus_polyphemus_HcB:0.236641,(((Mastigoproctus_giganteus_HcB:0.166817,Euphrynichus_bacillifer_HcB:0.169694):0.073455,(Euphrynichus_bacillifer_HcA:0.177724,Mastigoproctus_giganteus_HcA:0.225879):0.099439):0.1045,Limulus_polyphemus_HcA:0.219198):0.124566):0.042795):0.530544,(Polysphondylium_pallidum_tyr2:0.15858,Dictyostelium_fasciculatum_tyr:0.135047):1.181737):0.271301,(((('Ciona_intestinalis tyr4':0.0,Ciona_intestinalis_tyr3:0.0):4.0E-6,Ciona_intestinalis_tyr2:0.033922):0.57079,Ciona_intestinalis_tyr1:0.568672):0.233287,Saccoglossus_kowaleksii_Hc:0.425366):0.863477):0.587056,Amphimedon_queenslandica_tyr:0.395724):0.878089,Aspergillus_nidulans_tyr1:0.0,Aspergillus_nidulans_tyr2:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61736] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_1 = [&R] ((((((((((((((Anopheles_gambiae_tyr2:0.233091,Anopheles_gambiae_tyr8:0.153654):0.156464,Anopheles_gambiae_tyr9:0.402346):0.039061,(Anopheles_gambiae_tyr7:0.064713,Anopheles_gambiae_tyr5:0.047764):0.278448):0.068049,(Anopheles_gambiae_tyr4:0.260496,(Anopheles_gambiae_tyr3:0.182707,Anopheles_gambiae_tyr6:0.281033):0.113732):0.036914):0.058175,Drosophila_melanogaster_tyr3:0.303112):0.1195,((Bombyx_mori_tyr2:0.559166,Bombyx_mori_tyr1:0.370246):0.089918,(((Tribolium_castaneum_tyr3:0.005329,Tribolium_castaneum_tyr2:0.0):0.138557,Tribolium_castaneum_tyr1:0.266644):0.084191,(Drosophila_melanogaster_tyr2:0.180732,Drosophila_melanogaster_tyr1:0.191931):0.084817):0.038847):0.084738):0.039219,Anopheles_gambiae_tyr1:0.353066):0.198468,Daphnia_pulex_tyr:0.472907):0.178866,(Limulus_polyphemus_HcB:0.311385,((Limulus_polyphemus_HcA:0.278235,(Mastigoproctus_giganteus_HcA:0.196749,Euphrynichus_bacillifer_HcA:0.158054):0.099493):0.075719,(Mastigoproctus_giganteus_HcB:0.169832,Euphrynichus_bacillifer_HcB:0.18264):0.076371):0.124614):0.15271):0.189175,Epiperipatus_sp_Hc:0.623279):0.307892,(Polysphondylium_pallidum_tyr2:0.154024,Dictyostelium_fasciculatum_tyr:0.183096):1.014593):0.697083,(((Ciona_intestinalis_tyr2:0.006687,('Ciona_intestinalis tyr4':0.0,Ciona_intestinalis_tyr3:0.0):0.025089):0.662318,Ciona_intestinalis_tyr1:0.522331):0.263538,Saccoglossus_kowaleksii_Hc:0.613343):0.571944):0.444549,Amphimedon_queenslandica_tyr:0.622413):0.738655,Aspergillus_nidulans_tyr1:0.0,Aspergillus_nidulans_tyr2:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61729] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_18 = [&R] (((((((((((Anopheles_gambiae_tyr3:0.249514,Anopheles_gambiae_tyr6:0.287811):0.17797,(Anopheles_gambiae_tyr9:0.381022,(Anopheles_gambiae_tyr8:0.12505,Anopheles_gambiae_tyr2:0.297254):0.167459):0.078973):0.063226,(((Anopheles_gambiae_tyr5:0.040035,Anopheles_gambiae_tyr7:0.089266):0.246478,Anopheles_gambiae_tyr4:0.272374):0.061234,Drosophila_melanogaster_tyr3:0.336912):0.052938):0.128127,((((Drosophila_melanogaster_tyr2:0.137583,Anopheles_gambiae_tyr1:0.345492):0.103081,Drosophila_melanogaster_tyr1:0.252575):0.063756,((Tribolium_castaneum_tyr3:0.00541,Tribolium_castaneum_tyr2:0.0):0.143055,Tribolium_castaneum_tyr1:0.290319):0.07669):0.086205,(Bombyx_mori_tyr2:0.527229,Bombyx_mori_tyr1:0.375127):0.06505):0.136612):0.168233,Daphnia_pulex_tyr:0.71114):0.157608,(((Mastigoproctus_giganteus_HcB:0.188864,((Mastigoproctus_giganteus_HcA:0.25304,Euphrynichus_bacillifer_HcA:0.195756):0.116762,Limulus_polyphemus_HcA:0.252616):0.068808):0.031794,Euphrynichus_bacillifer_HcB:0.273377):0.204853,Limulus_polyphemus_HcB:0.253493):0.290339):0.079455,Epiperipatus_sp_Hc:0.705901):0.493709,(Dictyostelium_fasciculatum_tyr:0.163735,Polysphondylium_pallidum_tyr2:0.137656):0.927827):0.537439,((((Ciona_intestinalis_tyr3:0.0,'Ciona_intestinalis tyr4':0.0):1.0E-6,Ciona_intestinalis_tyr2:0.011598):0.819092,Ciona_intestinalis_tyr1:0.578316):0.383874,Saccoglossus_kowaleksii_Hc:0.630678):0.755068):0.363279,Amphimedon_queenslandica_tyr:0.764392):1.035473,Aspergillus_nidulans_tyr1:0.0,Aspergillus_nidulans_tyr2:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61746] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_28 = [&R] (((((((((((((((Anopheles_gambiae_tyr6:0.327929,Anopheles_gambiae_tyr3:0.192617):0.152658,Drosophila_melanogaster_tyr3:0.425875):0.099338,(((Anopheles_gambiae_tyr5:0.027102,Anopheles_gambiae_tyr7:0.089304):0.219264,Anopheles_gambiae_tyr9:0.361386):0.056136,(Anopheles_gambiae_tyr2:0.270581,Anopheles_gambiae_tyr8:0.134503):0.171118):0.046354):0.037851,Anopheles_gambiae_tyr4:0.265014):0.188874,((Anopheles_gambiae_tyr1:0.328669,Drosophila_melanogaster_tyr2:0.109552):0.085528,Drosophila_melanogaster_tyr1:0.196792):0.087219):0.093562,(Tribolium_castaneum_tyr1:0.280216,(Tribolium_castaneum_tyr3:0.0,Tribolium_castaneum_tyr2:0.0):0.129486):0.088436):0.051361,Bombyx_mori_tyr2:0.480038):0.048092,Bombyx_mori_tyr1:0.366829):0.258166,Daphnia_pulex_tyr:0.582855):0.290366,Epiperipatus_sp_Hc:0.750591):0.200458,((Mastigoproctus_giganteus_HcB:0.179701,(Euphrynichus_bacillifer_HcB:0.196366,((Mastigoproctus_giganteus_HcA:0.241044,Euphrynichus_bacillifer_HcA:0.106896):0.135194,Limulus_polyphemus_HcA:0.220968):0.122631):0.045257):0.143499,Limulus_polyphemus_HcB:0.337902):0.220313):0.457735,(Dictyostelium_fasciculatum_tyr:0.119577,Polysphondylium_pallidum_tyr2:0.220489):1.323728):0.639217,(((('Ciona_intestinalis tyr4':0.0,Ciona_intestinalis_tyr3:0.0):0.015112,Ciona_intestinalis_tyr2:0.020685):0.899882,Ciona_intestinalis_tyr1:0.53799):0.213978,Saccoglossus_kowaleksii_Hc:0.689322):0.975407):0.436512,Amphimedon_queenslandica_tyr:0.691606):1.197913,Aspergillus_nidulans_tyr1:0.0,Aspergillus_nidulans_tyr2:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61756] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_23 = [&R] (((((((((((Anopheles_gambiae_tyr4:0.217203,(Anopheles_gambiae_tyr7:0.094058,Anopheles_gambiae_tyr5:0.053704):0.209672):0.046673,Drosophila_melanogaster_tyr3:0.370731):0.049434,(((Anopheles_gambiae_tyr8:0.156989,Anopheles_gambiae_tyr2:0.241153):0.200257,Anopheles_gambiae_tyr9:0.33459):0.064971,(Anopheles_gambiae_tyr3:0.219912,Anopheles_gambiae_tyr6:0.302882):0.193863):0.066909):0.132457,(((Bombyx_mori_tyr2:0.536211,Bombyx_mori_tyr1:0.357918):0.099231,((Tribolium_castaneum_tyr2:0.0,Tribolium_castaneum_tyr3:0.002711):0.087613,Tribolium_castaneum_tyr1:0.289152):0.067748):0.021286,((Drosophila_melanogaster_tyr2:0.119318,Drosophila_melanogaster_tyr1:0.230165):0.078628,Anopheles_gambiae_tyr1:0.24777):0.110094):0.079068):0.139476,Daphnia_pulex_tyr:0.524718):0.241558,Epiperipatus_sp_Hc:0.613707):0.08516,((((Euphrynichus_bacillifer_HcA:0.18965,Mastigoproctus_giganteus_HcA:0.161079):0.093237,(Mastigoproctus_giganteus_HcB:0.124666,Euphrynichus_bacillifer_HcB:0.186167):0.095856):0.073912,Limulus_polyphemus_HcA:0.205902):0.168563,Limulus_polyphemus_HcB:0.1951):0.168891):0.341089,(Dictyostelium_fasciculatum_tyr:0.118092,Polysphondylium_pallidum_tyr2:0.193237):0.738752):0.396952,((Ciona_intestinalis_tyr1:0.508398,(('Ciona_intestinalis tyr4':0.0,Ciona_intestinalis_tyr3:0.0):3.0E-6,Ciona_intestinalis_tyr2:0.035877):0.636238):0.320735,Saccoglossus_kowaleksii_Hc:0.690001):0.948783):0.403673,Amphimedon_queenslandica_tyr:0.642673):1.206775,Aspergillus_nidulans_tyr1:0.0,Aspergillus_nidulans_tyr2:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61751] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_25 = [&R] (((((((((((((Anopheles_gambiae_tyr8:0.13365,Anopheles_gambiae_tyr2:0.21143):0.138691,Anopheles_gambiae_tyr9:0.381056):0.074969,(Anopheles_gambiae_tyr5:0.053954,Anopheles_gambiae_tyr7:0.066635):0.178862):0.04839,((Anopheles_gambiae_tyr3:0.208228,Anopheles_gambiae_tyr6:0.305451):0.06944,Anopheles_gambiae_tyr4:0.249857):0.068137):0.024685,Drosophila_melanogaster_tyr3:0.318896):0.166908,((((Tribolium_castaneum_tyr3:0.0,Tribolium_castaneum_tyr2:0.0):0.157074,Tribolium_castaneum_tyr1:0.27146):0.064797,(((Drosophila_melanogaster_tyr2:0.108756,Anopheles_gambiae_tyr1:0.351845):0.103085,Drosophila_melanogaster_tyr1:0.189614):0.096323,Bombyx_mori_tyr1:0.435782):0.034817):0.037417,Bombyx_mori_tyr2:0.420998):0.149488):0.192199,Daphnia_pulex_tyr:0.591854):0.255396,(Limulus_polyphemus_HcB:0.2267,((Euphrynichus_bacillifer_HcB:0.164826,Mastigoproctus_giganteus_HcB:0.217438):0.067849,((Euphrynichus_bacillifer_HcA:0.149284,Mastigoproctus_giganteus_HcA:0.247313):0.097916,Limulus_polyphemus_HcA:0.244399):0.041687):0.157878):0.20771):0.215948,Epiperipatus_sp_Hc:0.537866):0.397394,(Polysphondylium_pallidum_tyr2:0.142619,Dictyostelium_fasciculatum_tyr:0.25372):1.242244):0.423597,((((Ciona_intestinalis_tyr3:0.0,'Ciona_intestinalis tyr4':0.0):0.0,Ciona_intestinalis_tyr2:0.026697):0.763535,Ciona_intestinalis_tyr1:0.623254):0.300484,Saccoglossus_kowaleksii_Hc:0.681305):0.958299):0.836531,Amphimedon_queenslandica_tyr:0.802114):1.063517,Aspergillus_nidulans_tyr1:0.0,Aspergillus_nidulans_tyr2:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61753] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_1000 = [&R] (((((((((((((Anopheles_gambiae_tyr8:0.105787,Anopheles_gambiae_tyr2:0.251871):0.157254,Anopheles_gambiae_tyr9:0.485257):0.065798,(Anopheles_gambiae_tyr5:0.042102,Anopheles_gambiae_tyr7:0.099494):0.191019):0.073906,((Anopheles_gambiae_tyr6:0.281173,Anopheles_gambiae_tyr3:0.178686):0.309564,Anopheles_gambiae_tyr4:0.250813):0.026742):0.103269,Drosophila_melanogaster_tyr3:0.250053):0.164165,(Bombyx_mori_tyr1:0.319928,(((Bombyx_mori_tyr2:0.462146,Tribolium_castaneum_tyr1:0.18219):0.10772,(Tribolium_castaneum_tyr2:0.0,Tribolium_castaneum_tyr3:0.005511):0.157258):0.113926,((Drosophila_melanogaster_tyr2:0.123617,Anopheles_gambiae_tyr1:0.424335):0.110028,Drosophila_melanogaster_tyr1:0.250276):0.084049):0.110797):0.077623):0.18972,Daphnia_pulex_tyr:0.478654):0.229709,Epiperipatus_sp_Hc:0.671599):0.150688,((Mastigoproctus_giganteus_HcB:0.198944,(Euphrynichus_bacillifer_HcB:0.154061,((Euphrynichus_bacillifer_HcA:0.152435,Mastigoproctus_giganteus_HcA:0.236905):0.12568,Limulus_polyphemus_HcA:0.218134):0.105894):0.033743):0.142766,Limulus_polyphemus_HcB:0.229691):0.164709):0.465726,(Polysphondylium_pallidum_tyr2:0.129622,Dictyostelium_fasciculatum_tyr:0.203252):0.83341):0.474052,((Ciona_intestinalis_tyr1:0.537035,((Ciona_intestinalis_tyr3:0.0,'Ciona_intestinalis tyr4':0.0):0.027675,Ciona_intestinalis_tyr2:0.014549):0.806304):0.335851,Saccoglossus_kowaleksii_Hc:0.400281):1.046181):0.435105,Amphimedon_queenslandica_tyr:0.825851):0.886805,Aspergillus_nidulans_tyr1:0.0,Aspergillus_nidulans_tyr2:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61757] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_21 = [&R] (((((((((((((Drosophila_melanogaster_tyr2:0.120787,Drosophila_melanogaster_tyr1:0.206097):0.066747,Anopheles_gambiae_tyr1:0.268203):0.10395,((Tribolium_castaneum_tyr2:0.0,Tribolium_castaneum_tyr3:0.0):0.14523,Tribolium_castaneum_tyr1:0.203731):0.089077):0.035166,((((Anopheles_gambiae_tyr7:0.11081,Anopheles_gambiae_tyr5:0.058834):0.218699,(Anopheles_gambiae_tyr4:0.150802,(Anopheles_gambiae_tyr3:0.199595,Anopheles_gambiae_tyr6:0.337098):0.152031):0.085857):0.041578,((Anopheles_gambiae_tyr8:0.124575,Anopheles_gambiae_tyr2:0.232442):0.211973,Anopheles_gambiae_tyr9:0.39354):0.113563):0.025544,Drosophila_melanogaster_tyr3:0.256223):0.205296):0.020903,Bombyx_mori_tyr2:0.388454):0.052163,Bombyx_mori_tyr1:0.333858):0.212101,Daphnia_pulex_tyr:0.578913):0.133251,Epiperipatus_sp_Hc:0.819257):0.277943,((((Mastigoproctus_giganteus_HcB:0.217645,Euphrynichus_bacillifer_HcB:0.145601):0.112111,(Mastigoproctus_giganteus_HcA:0.206084,Euphrynichus_bacillifer_HcA:0.094758):0.107203):0.052304,Limulus_polyphemus_HcA:0.213803):0.107023,Limulus_polyphemus_HcB:0.247103):0.102939):0.612925,(Polysphondylium_pallidum_tyr2:0.060585,Dictyostelium_fasciculatum_tyr:0.192515):1.32864):0.3832,(((Ciona_intestinalis_tyr2:2.0E-6,('Ciona_intestinalis tyr4':0.0,Ciona_intestinalis_tyr3:0.0):0.024678):0.574407,Ciona_intestinalis_tyr1:0.548743):0.402722,Saccoglossus_kowaleksii_Hc:0.454958):1.002451):0.619019,Amphimedon_queenslandica_tyr:0.653264):1.010916,Aspergillus_nidulans_tyr1:0.0,Aspergillus_nidulans_tyr2:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61749] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_3 = [&R] (((((((((((((Tribolium_castaneum_tyr2:0.0,Tribolium_castaneum_tyr3:0.002564):0.156107,Tribolium_castaneum_tyr1:0.244165):0.061894,(Bombyx_mori_tyr1:0.381183,((Drosophila_melanogaster_tyr2:0.061437,Anopheles_gambiae_tyr1:0.36377):0.097665,Drosophila_melanogaster_tyr1:0.237352):0.054582):0.075855):0.056692,Bombyx_mori_tyr2:0.450186):0.051547,((((Anopheles_gambiae_tyr6:0.245048,Anopheles_gambiae_tyr3:0.287308):0.161564,((Anopheles_gambiae_tyr2:0.273489,Anopheles_gambiae_tyr8:0.127659):0.127889,Anopheles_gambiae_tyr9:0.377025):0.032034):0.154537,(Drosophila_melanogaster_tyr3:0.337728,(Anopheles_gambiae_tyr7:0.133608,Anopheles_gambiae_tyr5:0.034976):0.190955):0.084281):0.043869,Anopheles_gambiae_tyr4:0.24231):0.157868):0.127408,Daphnia_pulex_tyr:0.610168):0.191326,Epiperipatus_sp_Hc:0.772709):0.185308,Limulus_polyphemus_HcB:0.282404):0.045951,((Limulus_polyphemus_HcA:0.271288,(Mastigoproctus_giganteus_HcA:0.295096,Euphrynichus_bacillifer_HcA:0.185955):0.072356):0.071196,(Mastigoproctus_giganteus_HcB:0.196415,Euphrynichus_bacillifer_HcB:0.107356):0.147701):0.10853):0.462362,(Polysphondylium_pallidum_tyr2:0.11395,Dictyostelium_fasciculatum_tyr:0.214466):0.880362):0.459843,(Saccoglossus_kowaleksii_Hc:0.55332,((Ciona_intestinalis_tyr2:0.030126,(Ciona_intestinalis_tyr3:0.0,'Ciona_intestinalis tyr4':0.0):1.0E-6):0.68115,Ciona_intestinalis_tyr1:0.619745):0.291118):0.956914):0.641001,Amphimedon_queenslandica_tyr:0.575846):0.951172,Aspergillus_nidulans_tyr1:0.0,Aspergillus_nidulans_tyr2:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61731] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_12 = [&R] ((((((((((((Bombyx_mori_tyr2:0.4847,Tribolium_castaneum_tyr1:0.167971):0.100041,(Tribolium_castaneum_tyr3:0.0,Tribolium_castaneum_tyr2:0.0):0.080815):0.053682,((Drosophila_melanogaster_tyr2:0.085333,Anopheles_gambiae_tyr1:0.272383):0.093902,Drosophila_melanogaster_tyr1:0.202425):0.114721):0.041587,Bombyx_mori_tyr1:0.412799):0.070518,((Anopheles_gambiae_tyr4:0.226883,((Anopheles_gambiae_tyr7:0.0952,Anopheles_gambiae_tyr5:0.060689):0.199087,((Anopheles_gambiae_tyr3:0.214858,Anopheles_gambiae_tyr6:0.248186):0.167478,((Anopheles_gambiae_tyr8:0.11546,Anopheles_gambiae_tyr2:0.201097):0.119685,Anopheles_gambiae_tyr9:0.322232):0.044933):0.084118):0.066725):0.100366,Drosophila_melanogaster_tyr3:0.262898):0.062648):0.163334,Daphnia_pulex_tyr:0.633715):0.332489,((((Mastigoproctus_giganteus_HcA:0.224159,Euphrynichus_bacillifer_HcA:0.189007):0.103256,(Euphrynichus_bacillifer_HcB:0.216459,Mastigoproctus_giganteus_HcB:0.097405):0.077534):0.113472,Limulus_polyphemus_HcA:0.164178):0.095016,Limulus_polyphemus_HcB:0.234266):0.23968):0.109008,Epiperipatus_sp_Hc:0.572667):0.239932,(Dictyostelium_fasciculatum_tyr:0.270534,Polysphondylium_pallidum_tyr2:0.076425):1.190885):0.620917,((Saccoglossus_kowaleksii_Hc:0.831034,Ciona_intestinalis_tyr1:0.552003):0.240772,(('Ciona_intestinalis tyr4':0.0,Ciona_intestinalis_tyr3:0.0):0.018995,Ciona_intestinalis_tyr2:0.015586):0.673231):0.854429):0.865224,Amphimedon_queenslandica_tyr:0.442487):1.317575,Aspergillus_nidulans_tyr1:0.0,Aspergillus_nidulans_tyr2:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61740] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_17 = [&R] (((((((((((Anopheles_gambiae_tyr6:0.263712,Anopheles_gambiae_tyr3:0.257479):0.145255,(Anopheles_gambiae_tyr2:0.243096,Anopheles_gambiae_tyr8:0.11434):0.180984):0.055749,Anopheles_gambiae_tyr9:0.329959):0.076911,((Anopheles_gambiae_tyr4:0.244627,(Anopheles_gambiae_tyr5:0.04426,Anopheles_gambiae_tyr7:0.100797):0.161527):0.058373,Drosophila_melanogaster_tyr3:0.364302):0.036122):0.127252,(((Tribolium_castaneum_tyr1:0.253813,Bombyx_mori_tyr2:0.389471):0.099044,(((Anopheles_gambiae_tyr1:0.365741,Drosophila_melanogaster_tyr2:0.08744):0.154753,Drosophila_melanogaster_tyr1:0.181611):0.077939,(Tribolium_castaneum_tyr3:0.00279,Tribolium_castaneum_tyr2:0.0):0.138477):0.046367):0.048266,Bombyx_mori_tyr1:0.420033):0.096406):0.215017,(Daphnia_pulex_tyr:0.503497,Epiperipatus_sp_Hc:0.70516):0.136225):0.261346,((((Mastigoproctus_giganteus_HcA:0.224653,Euphrynichus_bacillifer_HcA:0.190744):0.106382,Limulus_polyphemus_HcA:0.209074):0.073093,(Euphrynichus_bacillifer_HcB:0.188648,Mastigoproctus_giganteus_HcB:0.153957):0.084785):0.139366,Limulus_polyphemus_HcB:0.25288):0.190953):0.476449,(Dictyostelium_fasciculatum_tyr:0.149429,Polysphondylium_pallidum_tyr2:0.163521):0.849852):0.417791,(((('Ciona_intestinalis tyr4':0.0,Ciona_intestinalis_tyr3:0.0):0.021174,Ciona_intestinalis_tyr2:0.011795):0.646862,Ciona_intestinalis_tyr1:0.657891):0.234749,Saccoglossus_kowaleksii_Hc:0.535747):0.966982):0.728578,Amphimedon_queenslandica_tyr:0.762151):1.165486,Aspergillus_nidulans_tyr2:0.0,Aspergillus_nidulans_tyr1:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61745] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_24 = [&R] (((((((((((Anopheles_gambiae_tyr3:0.142259,Anopheles_gambiae_tyr6:0.374174):0.107909,(Anopheles_gambiae_tyr8:0.118241,Anopheles_gambiae_tyr2:0.218161):0.114595):0.055844,(((Anopheles_gambiae_tyr7:0.103306,Anopheles_gambiae_tyr5:0.047279):0.187055,Anopheles_gambiae_tyr4:0.252763):0.048897,Drosophila_melanogaster_tyr3:0.292011):0.04657):0.057477,Anopheles_gambiae_tyr9:0.358634):0.131061,(((Bombyx_mori_tyr1:0.374124,Bombyx_mori_tyr2:0.516153):0.083399,(Tribolium_castaneum_tyr1:0.226203,(Tribolium_castaneum_tyr3:0.002799,Tribolium_castaneum_tyr2:0.0):0.102387):0.078548):0.018018,(Drosophila_melanogaster_tyr1:0.152657,(Drosophila_melanogaster_tyr2:0.138579,Anopheles_gambiae_tyr1:0.314471):0.066891):0.063028):0.106486):0.231095,(Daphnia_pulex_tyr:0.455939,Epiperipatus_sp_Hc:0.693156):0.119149):0.154852,((((Euphrynichus_bacillifer_HcB:0.148642,Mastigoproctus_giganteus_HcB:0.201722):0.034008,(Mastigoproctus_giganteus_HcA:0.227808,Euphrynichus_bacillifer_HcA:0.135432):0.106203):0.084598,Limulus_polyphemus_HcA:0.205849):0.109737,Limulus_polyphemus_HcB:0.198767):0.147236):0.503616,(Dictyostelium_fasciculatum_tyr:0.085085,Polysphondylium_pallidum_tyr2:0.20273):1.379522):0.462466,((Ciona_intestinalis_tyr1:0.419467,(('Ciona_intestinalis tyr4':0.0,Ciona_intestinalis_tyr3:0.0):0.010754,Ciona_intestinalis_tyr2:0.010122):0.848385):0.172891,Saccoglossus_kowaleksii_Hc:0.45046):0.779461):0.457587,Amphimedon_queenslandica_tyr:0.743258):0.949749,Aspergillus_nidulans_tyr1:0.0,Aspergillus_nidulans_tyr2:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61752] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_6 = [&R] (((((((((((((Drosophila_melanogaster_tyr2:0.137555,Anopheles_gambiae_tyr1:0.244747):0.054752,Drosophila_melanogaster_tyr1:0.181116):0.059525,Bombyx_mori_tyr1:0.371351):0.039726,((Tribolium_castaneum_tyr3:0.0,Tribolium_castaneum_tyr2:0.0):0.091326,Tribolium_castaneum_tyr1:0.27983):0.090709):0.015387,Bombyx_mori_tyr2:0.608692):0.091908,((((Anopheles_gambiae_tyr3:0.238004,Anopheles_gambiae_tyr6:0.271352):0.126815,Anopheles_gambiae_tyr4:0.199985):0.036696,((Anopheles_gambiae_tyr5:0.046888,Anopheles_gambiae_tyr7:0.103133):0.217057,((Anopheles_gambiae_tyr8:0.111686,Anopheles_gambiae_tyr2:0.23461):0.154466,Anopheles_gambiae_tyr9:0.381419):0.05729):0.077068):0.056866,Drosophila_melanogaster_tyr3:0.382167):0.132405):0.165314,Daphnia_pulex_tyr:0.677045):0.132681,Epiperipatus_sp_Hc:0.826927):0.222271,((Limulus_polyphemus_HcA:0.186191,((Mastigoproctus_giganteus_HcB:0.210993,Euphrynichus_bacillifer_HcB:0.166388):0.123502,(Euphrynichus_bacillifer_HcA:0.164068,Mastigoproctus_giganteus_HcA:0.233593):0.078023):0.078639):0.217821,Limulus_polyphemus_HcB:0.164306):0.142313):0.537845,(Dictyostelium_fasciculatum_tyr:0.159874,Polysphondylium_pallidum_tyr2:0.116891):1.025014):0.353299,((((Ciona_intestinalis_tyr3:0.0,'Ciona_intestinalis tyr4':0.0):0.034296,Ciona_intestinalis_tyr2:2.18E-4):0.779429,Ciona_intestinalis_tyr1:0.583076):0.326386,Saccoglossus_kowaleksii_Hc:0.510398):1.089658):0.525055,Amphimedon_queenslandica_tyr:0.568942):0.962721,Aspergillus_nidulans_tyr2:0.0,Aspergillus_nidulans_tyr1:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61734] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_22 = [&R] (((((((((((Anopheles_gambiae_tyr4:0.227253,((Anopheles_gambiae_tyr5:0.075057,Anopheles_gambiae_tyr7:0.083854):0.231937,(((Anopheles_gambiae_tyr8:0.132696,Anopheles_gambiae_tyr2:0.200221):0.187103,Anopheles_gambiae_tyr9:0.38097):0.054632,(Anopheles_gambiae_tyr3:0.289556,Anopheles_gambiae_tyr6:0.273993):0.126595):0.086182):0.034643):0.076413,Drosophila_melanogaster_tyr3:0.358015):0.164481,Bombyx_mori_tyr1:0.518861):0.047739,((((Tribolium_castaneum_tyr2:0.0,Tribolium_castaneum_tyr3:0.002682):0.211835,Tribolium_castaneum_tyr1:0.289331):0.084181,((Drosophila_melanogaster_tyr2:0.088849,Anopheles_gambiae_tyr1:0.378862):0.133837,Drosophila_melanogaster_tyr1:0.271207):0.121872):0.086423,Bombyx_mori_tyr2:0.508167):0.050576):0.213903,Daphnia_pulex_tyr:0.625069):0.146762,((Limulus_polyphemus_HcA:0.196139,((Euphrynichus_bacillifer_HcA:0.180156,Mastigoproctus_giganteus_HcA:0.218995):0.114936,(Euphrynichus_bacillifer_HcB:0.181002,Mastigoproctus_giganteus_HcB:0.19825):0.087985):0.070796):0.116053,Limulus_polyphemus_HcB:0.297333):0.247923):0.134488,Epiperipatus_sp_Hc:0.565024):0.356167,(Dictyostelium_fasciculatum_tyr:0.260864,Polysphondylium_pallidum_tyr2:0.066182):1.043274):0.508589,(((Ciona_intestinalis_tyr2:0.018101,('Ciona_intestinalis tyr4':0.0,Ciona_intestinalis_tyr3:0.0):0.003141):0.6406,Ciona_intestinalis_tyr1:0.526784):0.426764,Saccoglossus_kowaleksii_Hc:0.666349):0.857872):0.673048,Amphimedon_queenslandica_tyr:0.432613):1.128516,Aspergillus_nidulans_tyr2:0.0,Aspergillus_nidulans_tyr1:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61750] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_14 = [&R] (((((((((Anopheles_gambiae_tyr9:0.398516,(((Drosophila_melanogaster_tyr3:0.38684,((Anopheles_gambiae_tyr5:0.054124,Anopheles_gambiae_tyr7:0.098235):0.191354,Anopheles_gambiae_tyr4:0.25163):0.036758):0.036008,(Anopheles_gambiae_tyr8:0.112902,Anopheles_gambiae_tyr2:0.261525):0.220432):0.060278,(Anopheles_gambiae_tyr6:0.269312,Anopheles_gambiae_tyr3:0.236201):0.206177):0.015857):0.167752,((Bombyx_mori_tyr2:0.418123,(((Tribolium_castaneum_tyr3:0.0,Tribolium_castaneum_tyr2:0.0):0.127788,Tribolium_castaneum_tyr1:0.31896):0.070552,((Anopheles_gambiae_tyr1:0.362055,Drosophila_melanogaster_tyr2:0.114675):0.125766,Drosophila_melanogaster_tyr1:0.238209):0.121884):0.085673):0.046044,Bombyx_mori_tyr1:0.44777):0.077448):0.108341,Daphnia_pulex_tyr:0.747453):0.154223,((Mastigoproctus_giganteus_HcA:0.209613,Euphrynichus_bacillifer_HcA:0.135037):0.114751,((Mastigoproctus_giganteus_HcB:0.190333,Euphrynichus_bacillifer_HcB:0.212023):0.094019,(Limulus_polyphemus_HcB:0.357535,Limulus_polyphemus_HcA:0.218162):0.1219):0.046844):0.324584):0.121802,Epiperipatus_sp_Hc:0.614572):0.466524,(Dictyostelium_fasciculatum_tyr:0.125906,Polysphondylium_pallidum_tyr2:0.245562):1.203412):0.373722,(Saccoglossus_kowaleksii_Hc:0.481802,((Ciona_intestinalis_tyr2:0.008173,(Ciona_intestinalis_tyr3:0.0,'Ciona_intestinalis tyr4':0.0):0.011315):0.804773,Ciona_intestinalis_tyr1:0.448646):0.156726):0.686555):0.597137,Amphimedon_queenslandica_tyr:0.780778):1.140175,Aspergillus_nidulans_tyr1:0.0,Aspergillus_nidulans_tyr2:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61742] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_2 = [&R] ((((((((((Anopheles_gambiae_tyr4:0.275475,((Anopheles_gambiae_tyr7:0.094839,Anopheles_gambiae_tyr5:0.04531):0.156076,Drosophila_melanogaster_tyr3:0.348046):0.077399):0.044626,((Anopheles_gambiae_tyr9:0.345908,(Anopheles_gambiae_tyr2:0.264895,Anopheles_gambiae_tyr8:0.096816):0.120075):0.066453,(Anopheles_gambiae_tyr3:0.218434,Anopheles_gambiae_tyr6:0.368029):0.130329):0.065064):0.120342,(((((Tribolium_castaneum_tyr3:0.005493,Tribolium_castaneum_tyr2:0.0):0.152013,Tribolium_castaneum_tyr1:0.211603):0.094447,Bombyx_mori_tyr2:0.380021):0.049798,(Drosophila_melanogaster_tyr1:0.185292,(Anopheles_gambiae_tyr1:0.363416,Drosophila_melanogaster_tyr2:0.10762):0.085297):0.095164):0.062327,Bombyx_mori_tyr1:0.375642):0.098375):0.223527,Daphnia_pulex_tyr:0.669659):0.187695,Epiperipatus_sp_Hc:0.823272):0.192749,((Limulus_polyphemus_HcA:0.190634,((Euphrynichus_bacillifer_HcB:0.18722,Mastigoproctus_giganteus_HcB:0.256047):0.112012,(Mastigoproctus_giganteus_HcA:0.319785,Euphrynichus_bacillifer_HcA:0.112556):0.094101):0.07316):0.065342,Limulus_polyphemus_HcB:0.31328):0.097567):0.433433,(Polysphondylium_pallidum_tyr2:0.239971,Dictyostelium_fasciculatum_tyr:0.086863):1.071375):0.36838,(Saccoglossus_kowaleksii_Hc:0.479721,(((Ciona_intestinalis_tyr3:0.0,'Ciona_intestinalis tyr4':0.0):0.028038,Ciona_intestinalis_tyr2:0.009095):0.762639,Ciona_intestinalis_tyr1:0.573666):0.268318):0.765991):0.48167,Amphimedon_queenslandica_tyr:0.886417):0.982193,Aspergillus_nidulans_tyr2:0.0,Aspergillus_nidulans_tyr1:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61730] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_27 = [&R] ((((((((((Tribolium_castaneum_tyr1:0.212968,Bombyx_mori_tyr2:0.500273):0.116684,(Tribolium_castaneum_tyr2:0.0,Tribolium_castaneum_tyr3:0.005425):0.165131):0.022771,(Bombyx_mori_tyr1:0.519498,((Anopheles_gambiae_tyr1:0.389783,Drosophila_melanogaster_tyr2:0.069679):0.144392,Drosophila_melanogaster_tyr1:0.185182):0.086456):0.05531):0.178483,((((Anopheles_gambiae_tyr9:0.33873,((Anopheles_gambiae_tyr2:0.232575,Anopheles_gambiae_tyr8:0.13832):0.179549,(Anopheles_gambiae_tyr6:0.346113,Anopheles_gambiae_tyr3:0.218969):0.171562):0.076354):0.075891,(Anopheles_gambiae_tyr5:0.060013,Anopheles_gambiae_tyr7:0.104268):0.175479):0.105071,Anopheles_gambiae_tyr4:0.18604):0.042235,Drosophila_melanogaster_tyr3:0.399899):0.124014):0.203012,(Daphnia_pulex_tyr:0.526811,Epiperipatus_sp_Hc:0.643487):0.202164):0.146603,((((Mastigoproctus_giganteus_HcA:0.215424,Euphrynichus_bacillifer_HcA:0.118852):0.115521,(Euphrynichus_bacillifer_HcB:0.198225,Mastigoproctus_giganteus_HcB:0.145983):0.147711):0.110914,Limulus_polyphemus_HcA:0.226857):0.161568,Limulus_polyphemus_HcB:0.280317):0.213113):0.314091,(Polysphondylium_pallidum_tyr2:0.190665,Dictyostelium_fasciculatum_tyr:0.171322):0.965779):0.299125,(((('Ciona_intestinalis tyr4':0.0,Ciona_intestinalis_tyr3:0.0):0.023899,Ciona_intestinalis_tyr2:1.0E-6):0.930219,Ciona_intestinalis_tyr1:0.510928):0.229321,Saccoglossus_kowaleksii_Hc:0.518925):0.976263):0.65452,Amphimedon_queenslandica_tyr:0.624294):1.030566,Aspergillus_nidulans_tyr2:0.0,Aspergillus_nidulans_tyr1:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61755] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_9 = [&R] ((((((((((((((Anopheles_gambiae_tyr2:0.312231,Anopheles_gambiae_tyr8:0.126279):0.183597,(Anopheles_gambiae_tyr7:0.089138,Anopheles_gambiae_tyr5:0.061475):0.160502):0.070744,(Anopheles_gambiae_tyr9:0.373729,(Anopheles_gambiae_tyr6:0.306662,Anopheles_gambiae_tyr3:0.206037):0.116499):0.064717):0.064461,Anopheles_gambiae_tyr4:0.276178):0.048205,Drosophila_melanogaster_tyr3:0.382173):0.155551,Bombyx_mori_tyr1:0.35526):0.046289,((((Drosophila_melanogaster_tyr2:0.110169,Drosophila_melanogaster_tyr1:0.275655):0.076599,Anopheles_gambiae_tyr1:0.26485):0.119405,((Tribolium_castaneum_tyr2:0.0,Tribolium_castaneum_tyr3:0.002781):0.126731,Tribolium_castaneum_tyr1:0.24657):0.061674):0.043333,Bombyx_mori_tyr2:0.424183):0.049291):0.214294,Daphnia_pulex_tyr:0.680216):0.094191,Epiperipatus_sp_Hc:0.673846):0.228246,((((Euphrynichus_bacillifer_HcB:0.175036,Mastigoproctus_giganteus_HcB:0.146318):0.082827,(Mastigoproctus_giganteus_HcA:0.236225,Euphrynichus_bacillifer_HcA:0.110214):0.114493):0.08812,Limulus_polyphemus_HcA:0.179672):0.140361,Limulus_polyphemus_HcB:0.154347):0.142489):0.446276,(Polysphondylium_pallidum_tyr2:0.130169,Dictyostelium_fasciculatum_tyr:0.164313):1.381606):0.308102,((((Ciona_intestinalis_tyr3:0.0,'Ciona_intestinalis tyr4':0.0):0.025511,Ciona_intestinalis_tyr2:0.010831):0.515337,Saccoglossus_kowaleksii_Hc:0.672238):0.212657,Ciona_intestinalis_tyr1:0.373766):1.05609):0.638862,Amphimedon_queenslandica_tyr:0.510067):1.024596,Aspergillus_nidulans_tyr2:0.0,Aspergillus_nidulans_tyr1:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61737] END; BEGIN TREES; TITLE Beta_ML; LINK TAXA = TaxaForAnalysisStep11031; TREE bootstrap_7 = [&R] (((((((((Anopheles_gambiae_tyr4:0.21747,((Anopheles_gambiae_tyr5:0.050856,Anopheles_gambiae_tyr7:0.072768):0.153806,Drosophila_melanogaster_tyr3:0.260401):0.08092):0.040386,((Anopheles_gambiae_tyr8:0.124406,Anopheles_gambiae_tyr2:0.221487):0.122539,((Anopheles_gambiae_tyr3:0.19341,Anopheles_gambiae_tyr6:0.299843):0.13212,Anopheles_gambiae_tyr9:0.271986):0.03679):0.069146):0.128919,(Daphnia_pulex_tyr:0.341796,Epiperipatus_sp_Hc:0.822439):0.270457):0.068217,((Bombyx_mori_tyr2:0.306443,Bombyx_mori_tyr1:0.351386):0.104318,(((Anopheles_gambiae_tyr1:0.301908,Drosophila_melanogaster_tyr2:0.087624):0.101976,Drosophila_melanogaster_tyr1:0.111255):0.089194,(Tribolium_castaneum_tyr1:0.255799,(Tribolium_castaneum_tyr3:0.002608,Tribolium_castaneum_tyr2:0.0):0.103815):0.073387):0.06822):0.060449):0.353717,(((Euphrynichus_bacillifer_HcA:0.087439,Mastigoproctus_giganteus_HcA:0.199088):0.070741,((Euphrynichus_bacillifer_HcB:0.120137,Mastigoproctus_giganteus_HcB:0.131416):0.092411,Limulus_polyphemus_HcA:0.202367):0.052366):0.157583,Limulus_polyphemus_HcB:0.24868):0.104598):0.385829,(Dictyostelium_fasciculatum_tyr:0.143309,Polysphondylium_pallidum_tyr2:0.132426):1.160429):0.304597,(((('Ciona_intestinalis tyr4':0.0,Ciona_intestinalis_tyr3:0.0):0.0,Ciona_intestinalis_tyr2:0.016942):0.612863,Ciona_intestinalis_tyr1:0.555001):0.266903,Saccoglossus_kowaleksii_Hc:0.704858):0.78931):0.537104,Amphimedon_queenslandica_tyr:0.614531):0.944442,Aspergillus_nidulans_tyr2:0.0,Aspergillus_nidulans_tyr1:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61735] END;