Description
Book SynopsisA comprehensive overview of Bayesian approaches to phylogenetics using Markov chain Monte Carlo (MCMC) methods, offering theoretical insight, pragmatic advice and tools to develop further models. This title is a one-stop reference to applying the latest phylogenetic models in BEAST 2, interpreting the analyses and extending these models further.
Trade Review'Want to construct a phylogeny, add in calibrated time points or work out the past history of an epidemic? The open source package BEAST has established itself as the industry standard for all this and more. This definitive book, explaining what is under the hood, how the user can customize extensions and, most critically, a simple 'how to' users guide, is necessary reading for beginners and specialists alike.' Laurence D. Hurst, University of Bath
'In concert with the dramatic improvements to DNA sequencing technology, Bayesian inference has revolutionized population genetics, phylogenetics, and divergence time estimation. A similar impact on epidemiology appears imminent via a suite of new Bayesian methods that incorporate host and pathogen DNA sequence data into established mathematical frameworks. This book is an accessible and thorough introduction to these Bayesian procedures. However, the book does far more than explain the theory. It also includes clear guides on how to use the BEAST 2 software for performing Bayesian analyses, and how to visualize the results. Because the software is designed to be extensible, the book instructs users to write their own code to supplement the diverse methods that are already implemented in BEAST 2. This book is timely and is written by two of the leaders of the field. I highly recommend it.' Jeff Thorne, North Carolina State University
Table of ContentsPreface; Acknowledgements; Part I. Theory: 1. Introduction; 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; Bibliography; List of authors; List of subjects.
