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Old 07-27-2014, 09:00 AM   #4
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Mothur can make a consensus from multiple sequences, but I'm not sure this approach will work very well; it doesn't do a very good job with highly divergent sequences. Still, worth trying. There's also PBDagCon (from PacBio) that generates a consensus from multiple sequences, though it is aimed at PacBio's error profiles rather than degenerate genes.
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