Phylogenetics and phylodynamics are central topics in modern biology. Phylogenetic inferences reconstruct the evolutionary relationships between organisms, whereas phylodynamic inferences reveal the dynamics that lead to the observed relationships. These two fields have many practical applications in disciplines such as epidemiology, developmental biology, paleontology, ecology and even linguistics. However phylogenetics and phylodynamics are complex and fast-evolving fields. As such, inference tools are not easily accessible to researchers who are not from a computational background.
BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. BEAST 2 includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results. A core aspect of the BEAST 2 design philosophy is to allow researchers to extend the core program without the involvement of the BEAST 2 developers. New methods are implemented as standalone packages that are developed and maintained separately of BEAST 2 itself.
BEAST 2 is a complex program and it is challenging to learn BEAST without the help of an expert. Workshops, summer schools and lectures are a great resource, but can only reach a handful of the people interested in performing BEAST analyses. Taming the BEAST is a platform for collecting a comprehensive set of BEAST 2 tutorials in one location. By providing a set of well-curated and up-to-date tutorials Taming the BEAST aims to fill this gap and provide researchers with the resources necessary to learn how to perform analyses in BEAST 2!
In keeping with the BEAST 2 design it is possible for anyone to extend or correct the set of tutorials on the website. Thus, Taming the BEAST relies on the community to curate tutorials and raise issues to ensure that all of the tutorials are up-to-date. Furthermore, it is possible for developers to upload tutorials to newly implemented packages. Finally, we also encourage anyone else with useful BEAST 2 teaching materials to upload them. Find out how you can contribute!
If you found Taming the BEAST helpful in designing your research, please cite the following paper:
Joëlle Barido-Sottani, Veronika Bošková, Louis du Plessis, Denise Kühnert, Carsten Magnus, Venelin Mitov, Nicola F. Müller, Jūlija Pečerska, David A. Rasmussen, Chi Zhang, Alexei J. Drummond, Tracy A. Heath, Oliver G. Pybus, Timothy G. Vaughan, Tanja Stadler (2018). Taming the BEAST – A community teaching material resource for BEAST 2. Systematic Biology, 67(1), 170–-174. doi: 10.1093/sysbio/syx060