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.

By contrast, Pairwise Sequence Alignment tools are used to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences.

Clustal Omega More Information & Help Documentation

New MSA tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments. Suitable for medium-large alignments.

Launch Clustal Omega

Kalign More Information & Help Documentation

Very fast MSA tool that concentrates on local regions. Suitable for large alignments.

Launch Kalign

MAFFT More Information & Help Documentation

MSA tool that uses Fast Fourier Transforms. Suitable for medium-large alignments.

Launch MAFFT

MUSCLE More Information & Help Documentation

Accurate MSA tool, especially good with proteins. Suitable for medium alignments.


MView More Information & Help Documentation

Transform a Sequence Similarity Search result into a Multiple Sequence Alignment or reformat a Multiple Sequence Alignment using the MView program.

Launch MView

T-Coffee More Information & Help Documentation

Consistency-based MSA tool that attempts to mitigate the pitfalls of progressive alignment methods. Suitable for small alignments.

Launch T-Coffee


The EBI has a new phylogeny-aware multiple sequence alignment program which makes use of evolutionary information to help place insertions and deletions.
Try it out at WebPRANK.

The tools described on this page are provided using Programmatic access to bioinformatics tools from EMBL-EBI update: 2017. If you have any feedback or encounter any issues please let us know via EMBL-EBI support.