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The quick reference evidence informed Muscle Manual is designed as a quick reference guide for health care students, therapist, practitioners, doctors & instructors, and as a companion to the Physical Assessment Manual, Orthopedic Conditions Manual and Physical Medicine Manual.
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You can also use the –clw command-line option to request output in CLUSTALW format, which is easier to understand for people. If muscle gives an error message and you don't know how to fix it, please read the Troubleshooting section. The default settings are designed to give the best accuracy, so this may be all you
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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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