title: Detecting and Analyzing Genetic Recombination Using RDP4.
abstract: Recombination between nucleotide sequences is a major process influencing the evolution of most species on Earth. The evolutionary value of recombination has been widely debated and so too has its influence on evolutionary analysis methods that assume nucleotide sequences replicate without recombining. When nucleic acids recombine, the evolution of the daughter or recombinant molecule cannot be accurately described by a single phylogeny. This simple fact can seriously undermine the accuracy of any phylogenetics-based analytical approach which assumes that the evolutionary history of a set of recombining sequences can be adequately described by a single phylogenetic tree. There are presently a large number of available methods and associated computer programs for analyzing and characterizing recombination in various classes of nucleotide sequence datasets. Here we examine the use of some of these methods to derive and test recombination hypotheses using multiple sequence alignments.
authors.affiliation: Institute of Infectious Diseases and Molecular Medicine, Computational Biology Group, University of Cape Town, Cape Town, 7549, South Africa. darrenpatrickmartin@gmail.com.
authors.forename: Darren P
authors.initials: DP
authors.lastname: Martin
authors.affiliation: Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
authors.forename: Ben
authors.initials: B
authors.lastname: Murrell
authors.affiliation: Institute of Infectious Diseases and Molecular Medicine, Computational Biology Group, University of Cape Town, Cape Town, 7549, South Africa.
authors.forename: Arjun
authors.initials: A
authors.lastname: Khoosal
authors.affiliation: Institute of Infectious Diseases and Molecular Medicine, Computational Biology Group, University of Cape Town, Cape Town, 7549, South Africa.
authors.forename: Brejnev
authors.initials: B
authors.lastname: Muhire
mesh_terms: D000465:Algorithms; D019143:Evolution, Molecular; D008957:Models, Genetic; D010802:Phylogeny; D011995:Recombination, Genetic / Q000235:genetics*
keywords: Breakpoints; Gene conversion; Phylogenetic trees; RDP4; Recombination