A multiple sequence alignment (MSA) is a method for the comparison of three or more biological sequences (protein, DNA, or RNA) by aligning them against each other. In practice, these query sequences would share an evolutionary relationship (common ancestor). With MSA the distances and similarities between the sequences can be inferred, which facilitates the analysis of phylogenetic association such as evolutionary origins.
A MSA allows to visualize the conserved locations in the sequences that hold the functional relevance across species as well as mutation events (that appear as hyphens in one or more of the sequences in the alignment) such as insertion, deletion mutations or sunstitutions to allow calculation the rate of evolution.
MSA is used to define a protein family by assessing sequence conservation of protein domains, tertiary and secondary structures.
