PMC

This diagram summarizes the flow of the MUSCLE algorithm. There are three main stages: Stage 1 (draft progressive), Stage 2 (improved progressive) and Stage 3 (refinement). A multiple alignment is available at the completion of each stage, at which point the algorithm may terminate.

Motifs misaligned by a progressive method. A set of 41 sequences containing SH2 domains () were aligned by the progressive method T-Coffee (above), and by MUSCLE (below). The N-terminal region of a subset of five sequences is shown. The highlighted columns (upper case) are conserved within this family but are misaligned by T-Coffee. It should be noted that T-Coffee aligns these motifs correctly when given these five sequences alone; the problem arises in the context of the other sequences. Complete alignments are available at http://www.drive5.com/muscle.