Statistical Methods in Molecular Evolution

Abstract

Markov models in molecular evolution.- Introduction to Applications of the Likelihood Function in Molecular Evolution.- Introduction to Markov Chain Monte Carlo Methods in Molecular Evolution.- Population Genetics of Molecular Evolution.- Maximum Likelihood Methods for Detecting Adaptive Protein Evolution.- HyPhy: Hypothesis Testing Using Phylogenies.- Bayesian Analysis of Molecular Evolution using MrBayes.- Estimation of divergence times from molecular sequence data.- Markov Models of Protein Sequence Evolution.- Models of Microsatellite Evolution.- Genome Rearrangement.- Phylogenetic Hidden Markov Models.- The Evolutionary Causes and Consequences of Base Composition Variation.- Statistical Alignment: Recent Progress, New Applications, and Challenges.- Estimating Substitution Matrices.- Posterior Mapping and Posterior Predictive Distributions.- Assessing the Uncertainty in Phylogenetic Inference.