Building evolutionary trees from sequence data. The Maximum Parsimony criteria, the special case of Perfect Phylogeny, and the Fitch-Hartigon dynamic program to minimize mutations when the tree and a sequence alignment are known.

Additive trees and their construction. The Neighbor-Joining algorithm and its use with near-additive data. Bootstrap values and their misuse.

Algorithms for constructing an Ultrametric Tree from an Ultrametric Matrix, and the relationship of ultrametrics to the molecular clock.