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. 2021:2231:3-16.
doi: 10.1007/978-1-0716-1036-7_1.

The Clustal Omega Multiple Alignment Package

Fabian Sievers  1 , Desmond G Higgins  2
Affiliations

The Clustal Omega Multiple Alignment Package

Fabian Sievers et al. Methods Mol Biol. 2021.

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.

Keywords: Clustal; Multiple sequence alignment; Progressive alignment; Protein sequences.

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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 - DOI - PubMed - PMC
    1. Higgins DG, Sharp PM (1988) CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73(1):237–244 - DOI
    1. Larkin MA, Blackshields G, Brown NP et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948 - DOI
    1. Higgins DG, Bleasby AJ, Fuchs R (1992) CLUSTAL V: improved software for multiple sequence alignment. Comput Appl Biosci 8(2):189–191 - PubMed
    1. 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 - DOI

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