Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm

The evolution of homologous sequences affected by recombination or gene conversion cannot be adequately explained by a single phylogenetic tree. Many tree-based methods for sequence analysis, for example, those used for detecting sites evolving nonneutrally, have been shown to fail if such phylogenetic incongruity is ignored. However, it may be possible to propose several phylogenies that can correctly model the evolution of nonrecombinant fragments. We propose a model-based framework that uses a genetic algorithm to search a multiple-sequence alignment for putative recombination break points, quantifies the level of support for their locations, and identifies sequences or clades involved in putative…

• UD
  U.S. Department of Veterans Affairs
• NI
  National Institutes of Health

  Awards: AI36214, AI43638, R01-GM66276, AI57167, AI47745
• CF
  Center for AIDS Research, University of Washington
• UO
  University of California, San Diego
• NI
  National Institute of Allergy and Infectious Diseases

  Awards: AI43638, AI36214