Multiple Alignment Program

MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. Default parameters are those that give the best average accuracy in our tests. Using versions current at the time of writing, my tests show that MUSCLE can achieve both better average accuracy and better speed than CLUSTALW or T‑Coffee, depending on the chosen options. Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.

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