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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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Write output in CLUSTALW format with the "CLUSTAL W (1.81)" header rather than the MUSCLE version. This is useful when a post-processing step is picky
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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
     

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