MUSCLE (alignment software)

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MUSCLE (multiple sequence comparison by log-expectation) is public domain, multiple sequence alignment software for protein and nucleotide sequences.[1][2]

MUSCLE is often used as a replacement for Clustal, since it typically (but not always) gives better sequence alignments; in addition, MUSCLE is significantly faster than Clustal, especially for larger alignments.[1][2]

MUSCLE is integrated into Geneious and MacVector and is also available in Sequencher and UGENE as a plugin.

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