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.
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References
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
Higgins DG, Sharp PM (1988) CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73(1):237–244
Larkin MA, Blackshields G, Brown NP et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948
Higgins DG, Bleasby AJ, Fuchs R (1992) CLUSTAL V: improved software for multiple sequence alignment. Comput Appl Biosci 8(2):189–191
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
Söding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951–960
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
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797
Sievers F, Hughes GM, Higgins DG (2014) Systematic Exploration of Guide-Tree Topology Effects for Small Protein Alignments. BMC Bioinformatics 15:338
Boyce K, Sievers F, Higgins DG (2014) Simple chained guide trees give high-quality protein multiple sequence alignments. PNAS 111(29):10556–10561
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
Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39(Suppl 2):W29–W37
Kimura M (1985) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
Durbin R, Eddy S, Krogh A, Mitchison G (1998) Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge University Press, Cambridge
Boyce K, Sievers F, Higgins DG (2015) Instability in progressive multiple sequence alignment algorithms. Algorithms Mol Biol 10:26
Lassmann T, Sonnhammer ELL (2005) Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 6:298
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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
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DOI: https://doi.org/10.1007/978-1-0716-1036-7_1
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