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dc.contributor.authorRasmussen, Matthew D.
dc.contributor.authorKellis, Manolis
dc.date.accessioned2012-05-25T17:07:45Z
dc.date.available2012-05-25T17:07:45Z
dc.date.issued2010-07
dc.identifier.issn0737-4038
dc.identifier.issn1537-1719
dc.identifier.urihttp://hdl.handle.net/1721.1/70947
dc.descriptionSupplementary tables S1, sections 2.1–2.3, and figures S1–S11 are available at Molecular Biology and Evolution online (http://www.mbe.oxfordjournals.org/).en_US
dc.description.abstractRecent sequencing and computing advances have enabled phylogenetic analyses to expand to both entire genomes and large clades, thus requiring more efficient and accurate methods designed specifically for the phylogenomic context. Here, we present SPIMAP, an efficient Bayesian method for reconstructing gene trees in the presence of a known species tree. We observe many improvements in reconstruction accuracy, achieved by modeling multiple aspects of evolution, including gene duplication and loss (DL) rates, speciation times, and correlated substitution rate variation across both species and loci. We have implemented and applied this method on two clades of fully sequenced species, 12 Drosophila and 16 fungal genomes as well as simulated phylogenies and find dramatic improvements in reconstruction accuracy as compared with the most popular existing methods, including those that take the species tree into account. We find that reconstruction inaccuracies of traditional phylogenetic methods overestimate the number of DL events by as much as 2–3-fold, whereas our method achieves significantly higher accuracy. We feel that the results and methods presented here will have many important implications for future investigations of gene evolution.en_US
dc.description.sponsorshipNational Science Foundation (U.S.) (CAREER award NSF 0644282)en_US
dc.language.isoen_US
dc.publisherOxford University Press (OUP)en_US
dc.relation.isversionofhttp://dx.doi.org/10.1093/molbev/msq189en_US
dc.rightsCreative Commons Attribution Non-Commercialen_US
dc.rights.urihttp://creativecommons.org/licenses/by-nc/2.5en_US
dc.sourceOxforden_US
dc.titleA Bayesian Approach for Fast and Accurate Gene Tree Reconstructionen_US
dc.typeArticleen_US
dc.identifier.citationRasmussen, M. D., and M. Kellis. “A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction.” Molecular Biology and Evolution 28.1 (2010): 273–290. Web. 25 May 2012.en_US
dc.contributor.departmentMassachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratoryen_US
dc.contributor.departmentMassachusetts Institute of Technology. Department of Electrical Engineering and Computer Scienceen_US
dc.contributor.approverKellis, Manolis
dc.contributor.mitauthorRasmussen, Matthew D.
dc.contributor.mitauthorKellis, Manolis
dc.relation.journalMolecular Biology and Evolutionen_US
dc.eprint.versionFinal published versionen_US
dc.type.urihttp://purl.org/eprint/type/JournalArticleen_US
eprint.statushttp://purl.org/eprint/status/PeerRevieweden_US
dspace.orderedauthorsRasmussen, M. D.; Kellis, M.en
mit.licensePUBLISHER_CCen_US
mit.metadata.statusComplete


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