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 sub.sample command can be used as a way to normalize your data, or to create a smaller set from your original set. It takes as an input the following file types: fasta, list, shared, rabund and sabund to generate a new file that contains a sampling of your original file.