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 cluster command assign sequences to OTUs (Operational Taxonomy Unit). The assignment is based on a phylip-formatted_distance_matrix or a column-formatted_distance_matrix and name file. It generates a list, a sabund (Species Abundance), and a rabund (Relative Abundance) file.