There are two versions of Clustal 2 multiple sequence alignment software: 1) Clustal W command-line tool and 2) Clustal X with graphical user interface.
Phylogeny; Sequence analysis; Nucleic acid sites, features and motifs; Nucleic acid structure analysis; Sequence sites, features and motifs
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
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