Alexei J. Drummond, Remco R. BouckaertCambridge University Press, 8/6/2015EAN 9781107019652, ISBN10: 1107019656Hardcover, 260 pages, 25 x 18 x 1.6 cmLanguage: EnglishWhat 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.PrefaceAcknowledgementsPart I. Theory1. Introduction2. Evolutionary trees3. Substitution and site models4. The molecular clock5. Structured trees and phylogeographyPart II. Practice6. Bayesian evolutionary analysis by sampling trees7. Setting up and running a phylogenetic analysis8. Estimating species trees from multilocus data9. Advanced analysis10. Posterior analysis and post-processing11. Exploring phylogenetic tree spacePart III. Programming12. Getting started with BEAST13. BEAST XML14. Coding and design patterns15. Putting it all togetherBibliographyList of authorsList of subjects.
