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MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation. MUSCLE is claimed to achieve both better average accuracy and better speed than ClustalW2 or T-Coffee, depending on the chosen options. can be found at Exonerate, BWA or BLAT. If you have any concerns, please contact us via support.
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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,.
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If muscle completes successfully, it will create a file seqs.afa containing the alignment. By default, output is created in "aligned FASTA" format (hence the .afa extension). This is just like regular FASTA except that gaps are added in order to align the sequences. This is a nice format for computers but not very readable for
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MUSCLE isn't really designed to support a nucleotide matrix, but you can hack it by pretending that AGCT are amino acids and making a 20x20 matrix out of the original 4x4 matrix. You MUST specify the -seqtype protein option to fool MUSCLE into believing that it is aligning amino acid sequences. For more information, see
     

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