Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure.

ABSTRACT: For sequences that are highly divergent, there is often insufficient information to infer accurate alignments, and phylogenetic uncertainty may be high. One way to address this issue is to make use of protein structural information, since structures generally diverge more slowly than sequences. In this work, we extend a recently developed stochastic model of pairwise structural evolution to multiple structures on a tree, analytically integrating over ancestral structures to permit efficient likelihood computations under the resulting joint sequence-structure model. We observe that the inclusion of structural information significantly reduces alignment and topology uncertainty, and reduces the number of topology and alignment errors in cases where the true trees and alignments are known. In

SUBMITTER: Herman JL 

PROVIDER: S-EPMC4137710 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature