Multiple Sequence Alignment: A Critical Comparison of Four Popular Programs

For both the computational biologist and the research biologist, the use of multiple sequence alignment (MSA) programs to simultaneously align multiple sequences of nucleic acids or proteins has become de rigueur. Successful alignments are used in a number of applications, such as (1) phylogenetic analysis, as a predictor of evolutionary relationships; (2) identifying conserved motifs and domains within related families of proteins that then may be inferred to play a role in structure and function; (3) structure prediction, in which the role of a residue in secondary or tertiary structure (e.g., α helix, β sheet, etc.,) is inferred.