Clustal Omega is the latest in the Clustal family of multiple sequence alignment tools, replacing ClustalW2 for protein or RNA alignments, or alignments of hundreds of sequences. Clustal Omega uses seeded guide trees and HMM profile-profile techniques to generate multiple sequence alignments.

Clustal Omega produces more acurate alignments, faster, than the older ClustalW tools, and allows alignment of hundreds of sequences in reasonable time.