Complex statistical modelling for phylogenetic inference

Molecular sequence data are a primary source of information about evolutionary relationships. Over the past few decades, there have been dramatic increases in the sizes of data available. Consequently, focus has shifted towards increasingly complex models that are less prone to the biases that are a consequence of model misspecification. At the same time, the computational challenges, which were always substantial, have become greater due to these increasingly complex models and larger data sizes. In this article, we review phylogenetic inference using sequence data and some recent advances in phylogenetic modelling. We discuss strategies for dealing with complex models, future challenges and paths forward.