Clustal Omega, accurate alignment of very large numbers of sequences

Methods Mol Biol. 2014;1079:105-16. doi: 10.1007/978-1-62703-646-7_6.


Clustal Omega is a completely rewritten and revised version of the widely used Clustal series of programs for multiple sequence alignment. It can deal with very large numbers (many tens of thousands) of DNA/RNA or protein sequences due to its use of the mBED algorithm for calculating guide trees. This algorithm allows very large alignment problems to be tackled very quickly, even on personal computers. The accuracy of the program has been considerably improved over earlier Clustal programs, through the use of the HHalign method for aligning profile hidden Markov models. The program currently is used from the command line or can be run on line.

MeSH terms

  • Computational Biology / methods*
  • Internet
  • Sequence Alignment / methods*
  • Software*
  • User-Computer Interface