Probabilistic Phylogenetic Inference with Insertions and Deletions 英文参考文献.docVIP

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Probabilistic Phylogenetic Inference with Insertions and Deletions 英文参考文献.doc

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Probabilistic Phylogenetic Inference with Insertions and Deletions 英文参考文献

ProbabilisticPhylogeneticInferencewithInsertionsand Deletions ElenaRivas*,SeanR.Eddy JaneliaFarmResearchCampus,HowardHughesMedicalInstitute,Ashburn,Virginia,UnitedStatesofAmerica Abstract Afundamentaltaskinsequenceanalysisistocalculatetheprobabilityofamultiplealignmentgivenaphylogenetictree relatingthesequencesandanevolutionarymodeldescribinghowsequenceschangeovertime.However,themostwidely used phylogenetic models only account for residue substitution events. We describe a probabilistic model of a multiple sequencealignmentthataccountsforinsertionanddeletioneventsinadditiontosubstitutions,givenaphylogenetictree, using a rate matrix augmented by the gap character. Starting from a continuous Markov process, we construct a non- reversiblegenerative(birth–death)evolutionarymodelforinsertionsanddeletions.Themodelassumesthatinsertionand deletioneventsoccuroneresidueatatime.Weapplythismodeltophylogenetictreeinferencebyextendingtheprogram DNAMLin PHYLIP.Usingstandardbenchmarkingmethodsonsimulateddataandanew‘‘concordancetest’’benchmarkonreal ribosomalRNAalignments,weshowthattheextendedprogramDNAMLeimprovesaccuracyrelativetotheusualapproachof ignoringgaps,whileretainingthecomputationalefficiencyoftheFelsensteinpeelingalgorithm. Citation: Rivas E, Eddy SR (2008) Probabilistic Phylogenetic Inference with Insertions and Deletions. PLoS Comput Biol 4(9): e1000172. doi:10.1371/ journal.pcbi.1000172 Editor:DavidHaussler,UniversityofCaliforniaSantaCruz,UnitedStatesofAmerica ReceivedOctober24,2007;AcceptedJuly31,2008;PublishedSeptember19,2008 Copyright: ? 2008 Rivas, Eddy. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:ThisworkwasfundedbytheHowardHughesMedicalInstitute. CompetingInterests:Theauthorshavedeclaredthatnocompetinginterestsexist. *E-mail:rivase@ Introduction models for ungapped alignment ana