Introduction

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)

Documentation

Help

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.

API

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)