Abstract
Summary Understanding the causes and consequences of genetic variation in human immunodeficiency virus (HIV) is one of the most important tasks facing medical and evolutionary biologists alike. A powerful analytical tool which is available to those working in this field is the phylogenetic tree, which describes the evolutionary relationships of the sequences in a sample and the history of the mutational events which separate them. Although phylogenetic trees of HIV are becoming commonplace, their use can be improved by tailoring the underlying statistical models to the idiosyncrasies of viral biology. The design and refinement of phylogenetic analyses consequently represents an important practical use of statistical methods in HIV research.
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