This background chapter summarizes some of the basic concepts used in molecular evolution, such as the use of Markov models in modelling sequence evolution as well as maximum-likelihood and Bayesian estimation. It also discusses comparisons of models and methods using likelihood-based tests, simulations, and empirical tests. The goal of this chapter is to provide consistent notation and common definitions, and to give the reader an introduction to those topics while avoiding repeated descriptions of the same concepts in several chapters.
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