Skip to main content

The Clustal Omega Multiple Alignment Package

  • Protocol
  • First Online:
Multiple Sequence Alignment

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2231))

Abstract

Clustal Omega is a version, completely rewritten and revised in 2011, 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 online.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 99.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 129.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Sievers F, Wilm A, Dineen D et al (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539. https://doi.org/10.1038/msb.2011.75

    Article  PubMed  PubMed Central  Google Scholar 

  2. Higgins DG, Sharp PM (1988) CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73(1):237–244

    Article  CAS  PubMed  Google Scholar 

  3. Larkin MA, Blackshields G, Brown NP et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948

    Article  CAS  PubMed  Google Scholar 

  4. Higgins DG, Bleasby AJ, Fuchs R (1992) CLUSTAL V: improved software for multiple sequence alignment. Comput Appl Biosci 8(2):189–191

    CAS  PubMed  Google Scholar 

  5. Blackshields G, Sievers F, Shi W et al (2010) Sequence embedding for fast construction of guide trees for multiple sequence alignment. Algorithms Mol Biol 5:21

    Article  PubMed  PubMed Central  Google Scholar 

  6. Söding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951–960

    Article  PubMed  Google Scholar 

  7. Arthur D, Vassilvitskii S (2007) k-means++: the advantages of careful seeding. Proceedings of the eighteenth annual ACM-SIAM symposium on discrete algorithms, Philadelphia, PA, pp. 1027–1035

    Google Scholar 

  8. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Sievers F, Hughes GM, Higgins DG (2014) Systematic Exploration of Guide-Tree Topology Effects for Small Protein Alignments. BMC Bioinformatics 15:338

    Article  PubMed  PubMed Central  Google Scholar 

  10. Boyce K, Sievers F, Higgins DG (2014) Simple chained guide trees give high-quality protein multiple sequence alignments. PNAS 111(29):10556–10561

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Chojnacki S, Cowley A, Lee J, Foix A, Lopez R (2017) Programmatic access to bioinformatics tools from EMBL-EBI update: 2017. Nucleic Acids Res 45(W1):W550–W553. https://doi.org/10.1093/nar/gkx273

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39(Suppl 2):W29–W37

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Kimura M (1985) The neutral theory of molecular evolution. Cambridge University Press, Cambridge

    Google Scholar 

  14. Durbin R, Eddy S, Krogh A, Mitchison G (1998) Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge University Press, Cambridge

    Book  Google Scholar 

  15. Boyce K, Sievers F, Higgins DG (2015) Instability in progressive multiple sequence alignment algorithms. Algorithms Mol Biol 10:26

    Article  PubMed  PubMed Central  Google Scholar 

  16. Lassmann T, Sonnhammer ELL (2005) Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 6:298

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Desmond G. Higgins .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Sievers, F., Higgins, D.G. (2021). The Clustal Omega Multiple Alignment Package. In: Katoh, K. (eds) Multiple Sequence Alignment. Methods in Molecular Biology, vol 2231. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1036-7_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-1036-7_1

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1035-0

  • Online ISBN: 978-1-0716-1036-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics