{PDF} Statistical Methods in Molecular Evolution Rasmus Nielsen

Markov models in molecular evolution / Nicolas Galtier, Olivier Gascuel, and Alain Jean-Marie — Introduction to applications of the likelihood function in molecular evolution / Jutta Buschbom and Arndt von Haeseler — 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 adaptive protein evolution / Joseph P. Bielawski and Ziheng Yang — HyPhy: hypothesis testing using phylogenies / Sergei L. Kosakovsky Pond and Spencer 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 Kishino — Markov models of protein sequence evolution / Matthew W. Dimmic — Models of microsatellite evolution / Peter Calabrese and Raazesh Sainudiin — Genome rearrangement / Rick Durrett — Phylogenetic hidden Markov models / Adam Siepel and David Haussler — The evolutionary causes and consequences of base composition variation / Gilean A.T. McVean — Statistical alignment: recent progress, new applications, and challenges / Gerton Lunter … [et al.] — Estimating substitution matrices / Von Bing Yap and Terry Speed — Posterior mapping and posterior predictive distributions / Jonathan P. Bollback — Assessing the uncertainty in phylogenetic inference / Hidetoshi Shimodaira and Masami Hasegawa