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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 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.
Part I. Theory
2. Evolutionary trees
3. Substitution and site models
4. The molecular clock
5. Structured trees and phylogeography
Part II. Practice
6. Bayesian evolutionary analysis by sampling trees
7. Setting up and running a phylogenetic 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
13. BEAST XML
14. Coding and design patterns
15. Putting it all together
List of authors
List of subjects
Alexei J. Drummond is Professor of Computational Biology and Principal Investigator at the Allan Wilson Centre of Molecular Ecology and Evolution at the University of Auckland, New Zealand. He is the lead author of the BEAST software package and has gained a reputation in the field as one of the most knowledgeable experts for Bayesian evolutionary analyses.
Remco R. Bouckaert is a computer scientist with a strong background in Bayesian methods. He is the main architect of version 2 of BEAST and has been working on extensions to the BEAST software and other phylogenetics projects in Alexei Drummond's group at the University of Auckland.