Bayesian Approaches to Phylogenetics

Shakespeare Early Editions: Computational Methods for Textual Studies

Introductory Reading

- Eddy, S.R., 2004. What is Bayesian statistics?. Nature biotechnology, 22(9), p.1177. Excellent brief introduction to Bayesian Statistics.

- Huelsenbeck, J.P., Ronquist, F., Nielsen, R. and Bollback, J.P., 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. science, 294(5550), pp.2310-2314. Good introduction to Bayesian approach to Phylogenetics

- "Bayesian inference takes a view of the phylogeny problem that makes analysis of large data sets more tractable: Instead of searching for the opti- mal tree, one samples trees according to their posterior probabili- ties. Once such a sample is available, features that are common among the trees can be dis- cerned. For example, the sample can be used to construct a consensus tree, with the posterior probabil- ity of the individual clades indicated on the tree. This is roughly equivalent to perform- ing a maximum likelihood analysis with bootstrap resampling (3), but much faster"

- Yang, Z. and Rannala, B., 2012. Molecular phylogenetics: principles and practice. Nature Reviews Genetics, 13(5), pp.303-314.

- SALEMI, M., VANDAMME, A.-M., & LEMEY, P. (2009). The phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing. Cambridge, UK, Cambridge University Press. Great in depth practical coverage of Phylogenetics