Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks.

Please note that Clustal Omega is currently a command line-only tool.

A full description of the algorithms used by Clustal Omega is available in the Molecular Systems Biology paper Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Latest additions to Clustal Omega are described in Clustal Omega for making accurate alignments of many protein sequences, general notes on Multiple Sequence Alignment can be found in Sievers, Barton and Higgins, Multiple Sequence Alignment, Bioinformatics 227, pp 227-250, AD Baxevanis, GD Bader, DS Wishart (Eds)


Clustal Omega can be run online at the following websites (this list will expand in the coming months).

Please that webservers may have limitations on maximum alignment size not present in the standalone version.

Download Clustal Omega

Source code

Installation instructions are available in the INSTALL file, once the archive is extracted. This release is intended for use with UNIX systems. Installation on Macs is also possible. Windows users should download the binary release below.

Precompiled binaries

Windows users should extract the zip file and read the enclosed INSTALL.txt. UNIX and Mac users should rename the downloaded file to clustalo and place in the location of their choice. This file may need to be made executable e.g.: chmod u+x clustalo


Please help us develop Clustal Omega by filling out a small questionnaire (11 pull-down menus + 1 text box, all optional, can be answered in a minute)


A Clustal Omega package is available for Gentoo Linux. A SlackBuilds package is also available for Slackware. A Debian package is available as part of Debian Med. A wrapper is available for EMBOSS.


We constructed two benchmark data-sets by blending existing structural alignment reference data-sets with homologous unaligned Pfam sequences.



Once you have installed Clustal Omega, type clustalo --help at a command prompt to see a brief overview of all options. A more comprehensive description is available in the README file.


The core functions of Clustal Omega are contained in a UNIX library (libclustalo) which can be used directly by other programs. The API for using libclustalo is automatically generated using Doxygen.

Citing 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 (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology 7:539 doi:10.1038/msb.2011.75

Sievers F, Higgins DG (2018) Clustal Omega for making accurate alignments of many protein sequences. Protein Sci 27:135-145

Sievers F, Barton GJ, Higgins DG (2020) Multiple Sequence Alignment. Bioinformatics 227, pp 227-250, AD Baxevanis, GD Bader, DS Wishart (Eds)

Contact / Bug reports

Clustal is currently maintained at the Conway Institute UCD Dublin by Des Higgins, Fabian Sievers, David Dineen, and Andreas Wilm. You can reach us at

View ChangeLog


SFI logo

Recent work on Clustal was funded by Science Foundation Ireland


2016-07-01  ·  Version 1.2.2 released. plugged memory leak, parallelised hhalign, more MAC-RAM.

2014-02-28  ·  Version 1.2.1 released. corrected Clustal format consensus line and label justification (multi-bit).

2013-06-12  ·  Version 1.2.0 released. turned off Kimura correction, added percentage identity.

2013-05-16  ·  Version 1.1.1 released. line-wrapping, old ClustalW format, cluster output, variable cluster-size, changes to distance matrix, output order.

2012-04-25  ·  Version 1.1.0 released. DNA/RNA support added.

2012-03-27  ·  Version 1.0.4 released.

2011-09-07  ·  Clustal Omega paper published in Molecular Systems Biology.

2011-09-07  ·  Version 1.0.3 released.

2011-06-23  ·  Version 1.0.2 released.

2011-06-20  ·  Version 1.0.1 released.

2011-06-16  ·  Version 1.0 released.