Inferring Trees

Molecular phylogenetics examines how biological sequences evolve and the historical relationships between them. An important aspect of many such studies is the estimation of a phylogenetic tree, which explicitly describes evolutionary relationships between the sequences. This chapter provides an introduction to evolutionary trees and some commonly used inferential methodology, focusing on the assumptions made and how they affect an analysis. Detailed discussion is also provided about some common algorithms used for phylogenetic tree estimation. Finally, there are a few practical guidelines, including how to combine multiple software packages to improve inference, and a comparison between Bayesian and maximum likelihood phylogenetics.