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 gave the best average benchmark accuracy in my tests. However, benchmark accuracy is a rather dubious measure
- Windows / Linux / Mac OsX
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Edgar, R.C. (2010)
Quality measures for protein alignment benchmarks
Nucleic Acids Res., 2010, 1–9.