Joint Bayesian Estimation of Phylogeny and Sequence Alignment

• Activity Number: 311
• Type: Topic Contributed
• Date/Time: Tuesday, August 4, 2009 : 10:30 AM to 12:20 PM
• Sponsor: WNAR
• Author(s): Heejung Shim*+ and Bret Larget
• Companies: University of Wisconsin-Madison and University of Wisconsin-Madison
• Keywords: Phylogeny ; alignment ; Bayesian approach

Abstract

Phylogeny and sequence alignment are estimated separately in the traditional techniques: first estimate a multiple sequence alignment, and then infer a phylogeny based on the sequence alignment estimated in the previous step. We develop a joint model for co-estimating phylogeny and sequence alignment which improves estimates from the traditional approach by accounting for uncertainty in the alignment in phylogenetic inferences. Unlike many models in common use, our indel model allows insertion and deletion (indel) events to involve more than one nucleotide base and to overlap each other. Since our method does not use dynamic programming, we expect computational advantages relative to alternative approaches. We employ a Bayesian approach using MCMC to estimate the joint posterior distribution of a phylogenetic tree and a multiple sequence alignment.