Bayesian Evolutionary Analysis with BEAST
Cambridge University Press, 8/6/2015
EAN 9781107019652, ISBN10: 1107019656
Hardcover, 260 pages, 25 x 18 x 1.6 cm
Language: English
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.
Preface
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.