For many genes a database search will reveal a whole number of homologous sequences. One then wishes to learn about the evolution and the sequence conservation in such a group. This question surpasses what can reasonably be achieved by the sequence comparison methods described in the previous section. Pairwise comparisons do not readily show positions that are conserved among a whole set of sequences and tend to miss subtle similarities that become visible when observed simultaneously among many sequences. Thus one wants to simultaneously compare several sequences.

In this section, we will briefly introduce the concept of multidimensional dynamic programming and heuristic algorithms, which allow for comparison of three (or more) biological sequences.