Bioinformatics pp 433-460 | Cite as

Detecting and Analyzing Genetic Recombination Using RDP4

  • Darren P. MartinEmail author
  • Ben Murrell
  • Arjun Khoosal
  • Brejnev Muhire
Part of the Methods in Molecular Biology book series (MIMB, volume 1525)


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.

Key words

Recombination Gene conversion Breakpoints Phylogenetic trees RDP4 


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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • Darren P. Martin
    • 1
    Email author
  • Ben Murrell
    • 2
  • Arjun Khoosal
    • 1
  • Brejnev Muhire
    • 1
  1. 1.Institute of Infectious Diseases and Molecular Medicine, Computational Biology GroupUniversity of Cape TownCape TownSouth Africa
  2. 2.Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaUSA

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