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.
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
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
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
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
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