Part I. Theory. 1. Introduction ; 2. Evolutionary trees ; 3. Substitution and site models ; 4. The molecular clock ; 5. Structured trees and phylogeny -- Part II. Practice. 6. Bayesian evolutionary analysis by sampling trees ; 7. Setting up and running a phylogentic analysis ; 8. Estimating species trees from multilocus data ; 9. Advanced analysis ; 10. Posterior analysis and post-processing ; 11. Exploring phylogenetic tree space -- Part III. Programming. 12. Getting started with BEAST 2 ; 13. BEAST XML ; 14. Coding and design patterns ; 15. Putting it all togenther.

What are the models used in phylogenetic analysis and what exactly is involved in Bayesian evolutionary analysis using Markov chain Monte Carlo (MCMC) methods? How can you choose and apply these models, which parameterisations and priors make sense, and how can you diagnose Bayesian MCMC when things go wrong? These are just a few of the questions answered in this comprehensive overview of Bayesian approaches to phylogenetics. This practical guide: • Addresses the theoretical aspects of the field • Advises on how to prepare and perform phylogenetic analysis • Helps with interpreting analyses and visualisation of phylogenies • Describes the software architecture • Helps developing BEAST 2.2 extensions to allow these models to be extended further. With an accompanying website providing example files and tutorials (http://beast2.org/), this one-stop reference to applying the latest phylogenetic models in BEAST 2 will provide essential guidance for all users - from those using phylogenetic tools, to computational biologists and Bayesian statisticians. Written by the lead authors of the BEAST software - it gives guidance on the theory and practice of Bayesian phylogenetic methods A foundation for making the leap from theory to practice with BEAST - the reader will learn how to develop their own evolutionary models and software extensions Examples files and downloadable resources for BEAST 2 - available at http://beast2.org/