Phylogenetics module of the Boston University Computational Immunology Summer School
After this course, I hope you will be able to
- understand basic features of evolutionary trees
- be familiar with the various types of tree inference, when they are useful, and their assumptions
- understand the basis of codon-based tests for natural selection.
Please download and make sure you can run seaview as soon as possible.
- FastTree – approximate ML
- RAxML, PhyML, and IQ-TREE – somewhat less approximate ML
- BEAST – Bayesian, inferring event times and rooted trees
- MrBayes and RevBayes – Bayesian, inferring unrooted trees
- DataMonkey, your one-stop online shop for selection and recombination analysis