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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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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
MUSCLE User Guide. Multiple sequence comparison by log-expectation. by Robert C. Edgar. Version 3.5. August 2004. /muscle. email: muscle (at) drive5.com.
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