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Clustal Omega

Clustal Omega

The original Clustal Omega tool for multiple protein sequence alignment. Clustal Omega is capable of aligning thousand of sequences and is an improvement of the previous version of Clustal, ClustalW and ClustalX, using HMMs, based on HHalign from Johannes Soeding. Clustal Omega also makes use of precomputed aligment information found in public databases.




  • Operation: Multiple sequence alignment
  • Input: Protein sequence in FASTA format
  • Output: FASTA,CLUSTAL, MSF, PHYLIP, SELEX,Stockholm, Vienna
  • Software interface: Web application; command-line user interface
  • Language: C
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL v2+
  • Cost: Free
  • Version name: 1.2.4
  • Maturity: Mature
  • Credit: Science Foundation Ireland
  • Contact: clustalw _at_
  • Collection: Clustal


Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG "Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega." Mol Syst Biol. 2011 Oct 11;7:539
PMID: 21988835
PMCID: PMC3261699

Sievers F, Higgins DG "Clustal Omega for making accurate alignments of many protein sciences." Protein Sci 27:135-145

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