CLUSTALÂ
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widely used multiple sequence alignment computer program. There are three main steps: 1) Do a pairwise alignment 2) Create a phylogenetic tree (or use a user-defined tree) 3) Use the phylogenetic tree to carry out a multiple alignment. CLUSTAL W is a further update of CLUSTAL which incorporates sequence weighting, position-specific gap penalties, and weight matrix choice. (Wikipedia, Edwards 2009)
