Accurate detection of recombinant breakpoints in whole-genome alignments.

ABSTRACT: We propose a novel method for detecting sites of molecular recombination in multiple alignments. Our approach is a compromise between previous extremes of computationally prohibitive but mathematically rigorous methods and imprecise heuristic methods. Using a combined algorithm for estimating tree structure and hidden Markov model parameters, our program detects changes in phylogenetic tree topology over a multiple sequence alignment. We evaluate our method on benchmark datasets from previous studies on two recombinant pathogens, Neisseria and HIV-1, as well as simulated data. We show that we are not only able to detect recombinant regions of vastly different sizes but also the location of breakpoints with great accuracy. We show that our method does well inferring recombination breakpoint

SUBMITTER: Westesson O 

PROVIDER: S-EPMC2651022 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature