This chapter is provided for the sake of completeness and reference. It can be skipped by readers who have a basic knowledge of phylogenetic analysis.

The comparison of biomolecular sequences is one of the most fundamental operations in computational biology. Two DNA or protein sequences that have a high similarity are usually presumed to be homologous, that is, to have evolved from a common ancestral sequence. Both high similarity and also homology of protein sequences often imply that the structure of the proteins is similar, which in turn usually implies that the proteins have a similar function.

Phylogenetic trees and networks are generally computed from aligned DNA or protein sequences and so the first step in an evolutionary study is often to build such an alignment.

Overview

Figure 2.1 shows the relationships between some of the main concepts introduced in this chapter. The focus of this chapter is on how to compute an alignment of molecular sequences. We discuss how to produce a pairwise alignment of two sequences. Then we focus on how to a compute multiple sequence alignment of a set of sequences using a progressive alignment approach.

Pairwise sequence alignment

The basic idea of alignment is to write two sequences one above the other so as to maximize the number of similar or identical bases or amino acids that occur underneath each other.