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

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

Launch Clustal Omega


EMBOSS Cons creates a consensus sequence from a protein or nucleotide multiple alignment.

Launch EMBOSS Cons


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

Launch Kalign


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

Launch MAFFT


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



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

Launch MView


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 Search and sequence analysis tools services from EMBL-EBI in 2022

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