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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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Installing MUSCLE · Making an alignment (MSA) · Creating a tree (N-J or UPGMA) · License: MUSCLE is public domain. MUSCLE papers, how to cite. Papers and citing MUSCLE Popular options and features. Alignment output formats · Adding a sequence to an existing MSA · Profile-profile alignment (aligning two MSAs)
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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