Multiple sequence alignments provide more information than pairwise alignments since they show conserved regions within a protein family which are of structural and functional importance.

What is the purpose of conducting a multiple sequence alignment?

Given a set of biological sequences (RNA, proteins, DNA), the purpose of a MSA method is to align the sequences in a way that will either reflect their evolutionary, functional or structural relationship (Figure 1).

How does multiple sequence alignment help in evolution?

Aligned sequences are used for many purposes, including estimation of patterns of divergence, selection, the tempo and mode of evolutionary change, identification of functional elements and constraints, and phylogenetic history, just to name a few.