In this chapter, we give a not-so-long and self-contained introduction to computational molecular evolution. In particular, we present the emergence of the use of likelihood-based methods, review the standard DNA substitution models, and introduce how model choice operates. We also present recent developments in inferring absolute divergence times and rates on a phylogeny, before showing how state-of-the-art models take inspiration from diffusion theory to link population genetics, which traditionally focuses at a taxonomic level below that of the species, and molecular evolution. Although this is not a cookbook chapter, we try and point to popular programs and implementations along the way.

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Methods in Molecular Biology
Department of Biology

Aris-Brosou, S. (Stéphane), & Rodrigue, N. (2019). A not-so-long introduction to computational molecular evolution. In Methods in Molecular Biology. doi:10.1007/978-1-4939-9074-0_3