Summary
The underlying assumption of the phylogenetic inference methods discussed in the previous chapter is that we have one set of hierarchical relationships among the taxa. While this approach is reasonable when applied to most DNA sequence alignments, it can be violated in certain bacteria and viruses due to sporadic recombination, which is a process whereby different strains exchange or transfer DNA subsequences. The present chapter discusses the implications of recombination for phylogenetic inference and describes various methods for detecting and identifying recombinant regions in sequence alignments.
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Husmeier, D., Wright, F. (2005). Detecting Recombination in DNA Sequence Alignments. In: Husmeier, D., Dybowski, R., Roberts, S. (eds) Probabilistic Modeling in Bioinformatics and Medical Informatics. Advanced Information and Knowledge Processing. Springer, London. https://doi.org/10.1007/1-84628-119-9_5
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DOI: https://doi.org/10.1007/1-84628-119-9_5
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