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Get.oturep (version
The distance method finds the sequence with the smallest maximum distance to other sequences. The abundance method chooses the most abundant sequence in the OTU as the representative.
Set this parameter to Yes if your distance matric might not fit in RAM

Mothur Overview

Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki.

Command Documentation

The get.oturep command generates a fasta-formatted sequence file containing only a representative sequence for each OTU. The opposite of the bin.seqs command.

v1.23.0: Updated to Mothur 1.33, added count and method parameter