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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
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
Popular multiple alignment software. MUSCLE is one of the most widely-used methods in biology. On average, MUSCLE is cited by ten new papers every day. Fast, accurate and easy to use. MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and
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