Bayesian Inference (Part 2: paper discussion)

Previous class check-up

• We studied Bayesian inference and focused on the main contributors to good or poor performance: priors, convergence and burnin.

Learning objectives

At the end of today’s session, you will be able to

• explain in details the MrBayes inference methods
• use MrBayes software

Pre-class work

• Read the papers corresponding to your group (in canvas):
  • MrBayes1 and MrBayes2
  • RevBayes

In-class discussion

Objective: Understand the method, assumptions and limitations of MrBayes software and Bayesian phylogenetics.

Instructions:

1. Separate group discussions (30 minutes): Students will discuss with their respective groups and prepare a 10-minute presentation for the whole class. Use the software cheatsheet as guideline for your discussion and presentation. Use these google slides:
   • MrBayes
   • RevBayes
2. Group presentations (20 minutes total; 10 minutes per group): Each group will summarize their discussion in a 10-minute presentation to the class.

Take-home message: always read carefully the paper and the documentation of any phylogenetic method you use

Create your own cheatsheet with description, strengths, weaknesses, assumptions and user choices (and other things you find relevant).