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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
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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The primary output is specified using the -out option, and defaults to standard output. Multiple output formats in one run. You can specify several -xxxout option on the same command line, which allows you to create multiple output formats in a single run, e.g.: muscle -in seqs.fa -fastaout seqs.afa -clwout seqs.aln