Multiple Sequence Alignment (MSA) is generally the alignment of three or more biological sequences (protein or nucleic acid) of similar length. From the output, homology can be inferred and the evolutionary relationships between the sequences studied. There are several online tools to make the comparative sequence analysis, out of which ClustalW, T-Coffee are the most commonly known and widely used.
Besides, there are several other MSA tools used for different purpose accessible at EBI like Clustal Omega (new MSA tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments and is used only for protein/amino acid sequences), MUSCLE (specially good with proteins, suitable for medium alignments), Kalign (fast MSA tool that concentrates on local regions and is suitable for large alignments), DbClustal (create a Multiple Sequence Alignment from a protein BLAST result ), MView (transform a Sequence Similarity Search result into a Multiple Sequence Alignment or reformat a Multiple Sequence Alignment ) and many more.
Crystallography 