Includes bibliographical references and index.

Markov models in molecular evolution / Nicolas Galtier, Olivier Gasc uel, and Alain Jean-Marie -- Introduction to applications of the likeli hood function in molecular evolution / Jutta Buschbom and Arndt von Hae seler -- Introduction to Markov chain Monte Carlo methods in molecular evolution / Bret Larget -- Population genetics of molecular evolution / Carlos D. Bustamante -- Maximum likelilhood methods for detecting adap tive protein evolution / Joseph P. Bielawski and Ziheng Yang -- HyPhy: hypothesis testing using phylogenies / Sergei L. Kosakovsky Pond and Sp encer V. Muse -- Bayesian analysis of molecular evolution using MrBayes / John P. Huelsenbeck and Fredrik Ronquist -- Estimation of divergence times from molecular sequence data / Jeffrey L. Thorne and Hirohisa Ki shino -- Markov models of protein sequence evolution / Matthew W. Dimmi c -- Models of microsatellite evolution / Peter Calabrese and Raazesh S ainudiin -- Genome rearrangement / Rick Durrett -- Phylogenetic hidden Markov models / Adam Siepel and David Haussler -- The evolutionary caus es and consequences of base composition variation / Gilean A.T. McVean -- Statistical alignment: recent progress, new applications, and challe nges / Gerton Lunter ... [et al.] -- Estimating substitution matrices / Von Bing Yap and Terry Speed -- Posterior mapping and posterior predic tive distributions / Jonathan P. Bollback -- Assessing the uncertainty in phylogenetic inference / Hidetoshi Shimodaira and Masami Hasegawa.