In the previous chapter, we considered the problem of multiple alignment of sets of sequences. One can argue [Sankoff, Morel & Cedergren 1973] that alignment of sequences should take account of their evolutionary relationship. For example, an alignment that implies many substitutions between closely related sequences is less plausible than one that makes most of its changes over large evolutionary distances.

Some multiple alignment algorithms use a tree; for instance, we have seen that several progressive alignment algorithms use a ‘guide tree’. As the name suggests, this tree is meant to guide the clustering process rather than satisfy a taxonomist. In this chapter we shift emphasis, and begin to take a serious interest in building trees. However, we do not lose sight of alignment: the last section describes methods for simultaneous alignment and tree building.

We concentrate here on two general approaches to tree building: distance methods and parsimony; the next chapter formulates phylogeny probabilistically.

The tree of life

The similarity of molecular mechanisms of the organisms that have been studied strongly suggests that all organisms on Earth had a common ancestor. Thus any set of species is related, and this relationship is called a phylogeny. Usually the relationship can be represented by a phylogenetic tree. The task of phylogenetics is to infer this tree from observations upon the existing organisms.

Traditionally, morphological characters (both from living and fossilised organisms) have been used for inferring phylogenies.