PPT Slide
The three basic steps in the CLUSTAL W approach are shared by all progressive alignment algorithms:
A. Calculate a matrix of pairwise distances based on pairwise alignments between the sequences
B. Use the result of A to build a guide tree, which is an inferred phylogeny for the sequences
C. Use the tree from B to guide the * of the sequences.
Our discussion comes from the paper Thompson et al, 1994.