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.

Citation
Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy
and high throughput, Nucleic Acids Research 32(5), 1792-97.