Sampling methods for phylogenetic inference with application to HIV

J.A. Stark, K. Tatsuoka and F. Seillier-Moiseiwitsch.

Fifth workshop on case studies in Bayesian statistics, Carnegie Mellon University, September 1999

Reconstructing phylogenies (evolutionary histories) of proteins from a set of observed sequences is an important statistical modelling task in molecular evolution. Maximum likelihood and Bayesian methods have been used for phylogenetic inference. We review Markov chain Monte Carlo schemes which have been developed, and discuss the application of these to HIV data. We consider the problem of analysing the results from one such sampler and describe in detail a method for determining a consensus labelled history. This is illustrated with an example of HIV protease.