Clustal Omega for making accurate alignments of many protein sequences

Protein Sci. 2018 Jan;27(1):135-145. doi: 10.1002/pro.3290. Epub 2017 Oct 30.


Clustal Omega is a widely used package for carrying out multiple sequence alignment. Here, we describe some recent additions to the package and benchmark some alternative ways of making alignments. These benchmarks are based on protein structure comparisons or predictions and include a recently described method based on secondary structure prediction. In general, Clustal Omega is fast enough to make very large alignments and the accuracy of protein alignments is high when compared to alternative packages. The package is freely available as executables or source code from or can be run on-line from a variety of sites, especially the EBI

Keywords: benchmarking; clustal omega; multiple sequence alignment; protein structure.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Proteins / chemistry
  • Proteins / genetics*
  • Sequence Alignment / methods*
  • Sequence Analysis, Protein / methods*
  • Software*


  • Proteins