Likelihood Calculation in Molecular Phylogenetics

Abstract

Abstract Likelihood estimation is central to many areas of the natural and physical sciences and has had a major impact on molecular phylogenetics. In this chapter we provide a concise review of some of the theoretical and computational aspects of likelihood-based phylogenetic inference. We outline the basic probabilistic model and likelihood computation algorithm, as well as extensions to more realistic models and strategics of likelihood optimization. We survey several of the theoretical underpinnings of the likelihood framework, reviewing research on consistency, identifiability, and the effect of model mis-specification, as well as advantages, and limitations, of likelihood ratio tests.