Phylogenetics of Hiv

A phylogeny is a set of relationships among groups of genes or organisms that reflects their evolutionary history. Inferring a phylogeny is an estimation procedure, a statistical inference of a true phylogenetic tree that is unknown. However, the aim of the phylogenetic analysis is not merely the reconstruction of a tree topology; the phylogeny provides a powerful framework in which several hypotheses can be tested and parameters of interest can be estimated from the data (Huelsenbeck and Crandall, 1997). Once a reliable estimate of the phylogeny of the sequences under study has been obtained, it can be used for testing diverse hypotheses about evolution. All phylogenetic methods are based on some set of assumptions. To understand the scope of the derived inferences, the assumptions of a method must be explained and delimited, and then tested and contrasted with the biological data at hand. Inferences derived from the phylogeny can be only as good as the phylogenetic estimate from which they were derived. There are many reasons why a clear understanding of the genetic relationships among different strains of a virus is desirable. Such knowledge can provide information on the origins and geographic distributions of particular strains, on their routes of transmission, and for the development of vaccines (Leigh Brown and Holmes, 1994). In the case of HIV, its rapid evolution provides an ideal system for a successful application of a variety of phylogenetic approaches, as evidenced by the increasing number of studies on HIV using phylogenies. Phylogenetic analyses of HIV sequences have been used to investigate a variety of problems (see Seiller