Tools for multiple protein sequence alignment. The algorithm uses a guide tree in alignment creation. There are two separate flavors of Clustal 2: Clustal W, the command-line version and Clustal X, the graphical version.
Proteomics
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG "Clustal W and Clustal X version 2.0." https://doi.org/10.1093/bioinformatics/btm404
PMID: 17846036
Higgins DG, Sharp PM "CLUSTAL: a package for performing multiple sequence alignment on a microcomputer" Gene, 73, 237-244 https://doi.org/10.1016/0378-1119(88)90330-7
PMID: 3243435
Higgins DG, Thompson JD, Gibson TJ "Using CLUSTAL for multiple sequence alignments" Methods Enzymol., 266, 383-402 https://doi.org/10.1016/S0076-6879(96)66024-8
PMID: 8743695
Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ "Multiple sequence alignment with Clustal X" Trends Biochem Sci., 23, 403-405 https://doi.org/10.1016/s0968-0004(98)01285-7
PMID: 9810230
Higgins,DG and Sharp,PM "Fast and sensitive multiple sequence alignments on a microcomputer" Comput. Appl. Biosci., 5, 151-153 https://doi.org/10.1093/bioinformatics/5.2.151
PMID: 2720464
Higgins DG, Bleasby AJ, Fuchs R "CLUSTAL V: improved software for multiple sequence alignment" Comput. Appl. Biosci., 8, 189-191 https://doi.org/10.1093/bioinformatics/8.2.189
PMID: 1591615
Thompson JD, Higgins DG, Gibson TJ "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice." Nucleic Acids Res. 1994 Nov 11;22(22):4673-80. https://doi.org/10.1093/nar/22.22.4673
PMID: 7984417
PMCID: PMC308517
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG "The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools" Nucleic Acids Res., 25, 4876-4882 https://doi.org/10.1093/nar/25.24.4876
PMID: 9396791
PMCID: PMC147148
Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD "Multiple sequence alignment with the Clustal series of programs" Nucleic Acids Res., 31, 3497-3500 https://doi.org/10.1093/nar/gkg500
PMID: 12824352
PMCID: PMC168907
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