Abstract
CLUSTAL is a package for performing fast and reliable automatic multiple alignment of many DNA or protein sequences. It was originally written for IBM-compatible microcomputers (1,2) and was later reorganized as a single program for VAX mainframes. Recently (3), the package was completely rewritten as a new program, CLUSTAL V, which is freely available for a wide variety of computer systems and which has a number of new features. The main improvements are the calculation of phylogenetic trees from sequence data sets with a bootstrap option for calculating confidence intervals on the groupings and the ability to align alignments with each other.
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References
Higgins, D. G. and Sharp, P. M (1988) CLUSTAL a package for performing multiple sequence alignments on a microcomputer. Gene 73, 237–244
Higgins, D. G. and Sharp, P. M (1989) Fast and sensitive multiple sequence alignments on a microcomputer. Comput. Applic. Biosci. 5, 151–153.
Higgins, D. G., Bleasby, A. J., and Fuchs, R. (1992) CLUSTAL V: improved software for multiple sequence alignment Comput. Applic. Biosci. 8, 189–191.
Feng, D.-F. and Doolittle, R F. (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol Evol 25, 351–360.
Wilbur, W J and Lipman, D. J (1983) Rapid similarity searches of nucleic acid and protein data banks. Proc. Natl Acad. Sci. USA 80, 726–730
Sneath, P. H. A. and Sokal, R R (1973) Numerical Taxonomy Freeman, San Francisco, CA.
Myers, E. W. and Miller, W. (1988) Optimal alignments in linear space Comput Applic. Biosci. 4, 11–17.
Dayhoff, M. O., Schwartz, R M., and Orcutt, B C (1978) in Atlas of Protein Sequence and Structure, vol. 5, supplement 3 (Dayhoff, M O, ed), NBRF, Washington, DC, p. 345.
Fuchs, R. (1990) Free molecular biological software available from the EMBL file server. Comput. Applic. Biosci 6, 120–121.
Bairoch, A. and Boeckmann, B. (1991) The SWIS-PROT protein sequence data bank. Nucleic Acids Res 19, 2247–2248.
Pearson, W. R. and Lipman, D. J. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad Sci. USA 85, 2444–2448
Barker, W. C, George, D G, Hunt, L T, and Garavelli, J. S. (1991) The PIR protein sequence database. Nucleic Acids Res. 16, 1869–1871
Felsenstein, J. (1985) Confidence limits on phylogenies. an approach using the bootstrap. Evolution 39, 783–791.
Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol 4, 406–425.
Kimura, M. (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111–120.
Kimura, M (1983) The Neutral Theory of Molecular Evolution Cambridge University Press, Cambridge, England.
Kernighan, B. W. and Ritchie, D. M. (1988) The C Programming Language. 2nd Ed, Prentice Hall, New Jersey
Devereux, J., Haeberli, P., and Smithies, O. (1984) A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12, 387–395.
Saitou, N. and Imanishi, T. (1989) Relative efficiencies of the Fitch-Margoliash, Maximum Parsimony, Maximum-Likelihood, Minimum-Evolution and Neighbor-Joining Methods of phylogenetic tree construction in obtaining the correct tree. Mol. Biol. Evol 6, 514–525
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© 1994 Humana Press Inc, Totowa, NJ
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Higgins, D.G. (1994). Clustal V: Multiple Alignment of DNA and Protein Sequences. In: Computer Analysis of Sequence Data. Methods in Molecular Biology, vol 25. Springer, Totowa, NJ. https://doi.org/10.1385/0-89603-276-0:307
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DOI: https://doi.org/10.1385/0-89603-276-0:307
Publisher Name: Springer, Totowa, NJ
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