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. 2004 Mar 19;32(5):1792–1797. doi: 10.1093/nar/gkh340

Figure 2.

Figure 2

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.