Distance-Based Methods

Distances between all pairs of species are determined.

If species are represented by DNA or protein sequences, the distances may depend on the number of substitutions, insertions and delitions needed to get one sequence from another.

Tree is computed from the resulting distance matrix such that the distances in the tree fit the distances in the matrix as good as possible.

A matrix and the corresponding tree is called additive if there is a perfect fit.

A matrix and the corresponding tree is called ultrametric if it is additive and if it is possible to place a root in the tree such that all distances from the root to the leaves are identical.

If an additive or ultrametric tree exists, it can be determined in polynomial time.