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Documentation · Support MUSCLE is one of the most widely-used methods in biology. On average, MUSCLE is cited by ten new papers every day.
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
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MUSCLE User Guide. Multiple sequence Edgar, Robert C (2004), MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
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