In this GitHub repository, you will find all the material that we will be using for the practical sessions focused on Bayesian inference. We will cover the following content:
- Day 1.a - Introduction to MCMC: we will use R to put in practice all the theoretical concepts that we have just gone through about Bayesian inference! You will learn how to write an algorithm to run MCMCs and how to run MCMC diagnostics: from assessing the effect of using different parameter values to evaluating chain efficiency and convergence.
- Day 1.b - Bayesian phylogenetic inference: we will infer a phylogeny using a Bayesian approach implemented in the program
MrBayes. We will explore the effect that choosing different priors, partitioning schemes, and nucleotide substitution models (among others) can have on phylogeny inference. - Day 2 - Divergence times estimation with PAML: we will use various in-house scripts and tools together with
BASEMLandMCMCtre, two programs that are part of the PAML software (Yang 2007), to run a Bayesian analysis for timetree inference using a node-dating approach and an approximation to the likelihood calculation implemented in MCMCtree (dos Reis and Yang, 2011) to speed up such analysis.
You can click the links you see above to navigate through the content of the practical sessions. Hope you enjoy them and... Happy inference! :)
ⓒ Dr Sandra Álvarez-Carretero | @sabifo4