At the end of this modules students will be able to:

Explain the basic principles of phylogenetic analysis: starting from a set of modern day sequences or characters, infer the tree that best explains their common evolutionary history, together with the estimated sequence of the ancestor, represented by the internal nodes in the tree.
Explain the principle of parsimony - the most likely tree is the one that minimizes changes during evolution.
Distinguish between small parsimony and large parsimony.
Use Sankoff's algorithm (small parsimony) to compute the parsimony score of a given tree.
Use Sankoff's algorithm, and backtracking, to compute the estimated ancestral characters at each node in a given tree.
Describe the difference between distance-based and character-based phylogenetic inference, including the fact that an efficient algorithm exists for computing the tree consistent with a distance matrix, if the matrix is additive.
Describe some differences between a generic hierarchical clustering algorithm and the neighbor-joining algorithm.