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.

Prerequisites

Please download and make sure you can run seaview as soon as possible.

Lecture: Phylogenetics methods intro to parsimony
Perform sequence alignment on sample data using seaview
Try using various algorithms to build trees with seaview; then try clicking “Full, Swap, Re-root, and Subtree”
Lecture: Likelihood methods in phylogenetics
Lecture: Phylogenetic confidence measures
Investigate a mysterious data set using aLRT and bootstrapping
Lecture: Codon models and tests for selection (part)
Lecture: Mutation and selection in B cells
Investigate tree balance (see Horns et al for an application of tree shape to B cells)

Inferring Phylogenies by Felsenstein
The Phylogenetic Handbook edited by Lemey, Salemi, and Vandamme, chapters by the stars