GARD: a genetic algorithm for recombination detection

MOTIVATION: Phylogenetic and evolutionary inference can be severely misled if recombination is not accounted for, hence screening for it should be an essential component of nearly every comparative study. The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments. RESULTS: We developed a likelihood-based model selection procedure that uses a genetic algorithm to search multiple sequence alignments for evidence of recombination breakpoints and identify putative recombinant sequences. GARD is an extensible and intuitive method that can be run efficiently in parallel.…

• 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