Bayesian Inference (Part 3: computer lab)
Instructions: Run MrBayes on the toy dataset described below. You can use my reproducible script as guideline: notebook-log.md.
New toy dataset: Download the data (algaemb.nex)
curl -O http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/data/algaemb.nex
You can also use the primates fasta file that you aligned with ClustalW, MUSCLE or T-Coffee.
Make sure to read the MrBayes tutorial carefully to determine the appropriate MrBayes block for your data.
Bonus points for paying attention to the importants aspects that affect the performance of the chosen method.
Double bonus points for comparing how do results differ if we use an alignment from a different method. That is, primatesAA-aligned-muscle.fasta are the aligned sequences with MUSCLE. I can run MrBayes on this file and on primatesAA-aligned.fasta which was aligned with ClustalW and compare with the estimated trees.
Homework
See the details of the Bayesian Inference HW in here.