title: GARD: a genetic algorithm for recombination detection.
abstract: BACKGROUND
  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. Extensive simulation studies show that the method nearly always outperforms other available tools, both in terms of power and accuracy and that the use of GARD to screen sequences for recombination ensures good statistical properties for methods aimed at detecting positive selection.
  
  
  BACKGROUND
  Freely available http://www.datamonkey.org/GARD/
authors.affiliation: Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA. spond@ucsd.edu
authors.forename: Sergei L
authors.initials: SL
authors.lastname: Kosakovsky Pond
authors.forename: David
authors.initials: D
authors.lastname: Posada
authors.forename: Michael B
authors.initials: MB
authors.lastname: Gravenor
authors.forename: Christopher H
authors.initials: CH
authors.lastname: Woelk
authors.forename: Simon D W
authors.initials: SD
authors.lastname: Frost
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D017124:Conserved Sequence / Q000235:genetics; D019143:Evolution, Molecular; D008957:Models, Genetic; D008969:Molecular Sequence Data; D011995:Recombination, Genetic / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software