What is multiple sequence alignment and when is it used?

Multiple sequence alignment (MSA) is the alignment of three or more biological sequences to identify conserved regions and patterns across related sequences. Common tools include ClustalW/Clustal Omega, MUSCLE, T-Coffee, and MAFFT. MSA is used for: identifying conserved functional domains, constructing phylogenetic trees, detecting evolutionary relationships, predicting protein secondary structure, designing degenerate primers for PCR, and identifying functional motifs. Progressive alignment methods build the MSA by first aligning the most similar sequences and progressively adding others.