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.

For details and citation:
Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high 
accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797. 
doi:10.1093/nar/gkh340
