The coalescent (Part 2: Computer lab)
Previous class check-up
- We studied the coalescent model on a species tree
Learning objectives
At the end of today’s session, you will be able to
- use ASTRAL and BUCKy software
Pre-class work
In-class exercise
Instructions: Run both coalescent software (ASTRAL and BUCKy).
We need multiple estimated gene trees (or estimated posterior distributions of gene trees from MrBayes) to run these methods. Both software provide toy data that we will use.
These steps are not added to the reproducible script: notebook-log.md. So, try to figure out the steps on your end and add them to your own reproducible script.
Homework
See the details of the Coalescent HW in here.
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).