A hierarchical model for incomplete alignments in phylogenetic inference.

ABSTRACT:

Motivation

Full-length DNA and protein sequences that span the entire length of a gene are ideally used for multiple sequence alignments (MSAs) and the subsequent inference of their relationships. Frequently, however, MSAs contain a substantial amount of missing data. For example, expressed sequence tags (ESTs), which are partial sequences of expressed genes, are the predominant source of sequence data for many organisms. The patterns of missing data typical for EST-derived alignments greatly compromise the accuracy of estimated phylogenies.

Results

We present a statistical method for inferring phylogenetic trees from EST-based incomplete MSA data. We propose a class of hierarchical models for modeling pairwise distances between the sequences, and develop a fully Bayesian ap

SUBMITTER: Cheng F 

PROVIDER: S-EPMC2647833 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature