Cipres Science Gateway

MUSCLE is public domain multiple alignment software for protein and nucleotide sequences. MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation. MUSCLE creates 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.

A manual for MUSCLE is available. [pdf]

MUSCLE home page here.

INPUT = dna or protein sequences in multiple fasta format (MFA).

Test input file (nucleic acid): muscle_seq_in.fasta

Test output file1 (alignment): muscle_output1.aln

Test output file2 (log file): muscle_logfile.txt

If you use MUSCLE, please cite: Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97. [pdf]

If there is a tool or a feature you need, please let us know.