May 26, 2018

MUltiple Sequence Comparison by Log-Expectation

MUSCLE is multiple alignment software for protein and nucleotide sequences. The name stands for multiple sequence comparison by log-expectation.

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 the published tests. MUSCLE can achieve both better average accuracy and better speed than CLUSTALW or T-Coffee, depending on the chosen options.


Edgar, R. C. 2004 MUSCLE multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 325 1792-1797.

Edgar, R. C. 2004 MUSCLE a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 51 113.

The NAR paper gives only a brief overview of the algorithm and implementation details. For a full discussion of the method and many of the non-default options that it offers, please see the BMC paper.

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