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.
The bin.seqs command generates fasta-formatted files where sequences are ordered according to the OTU from the list_file that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences.