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 summary.single command produce a summary file that has the calculator value for each line in the OTU data and for all possible comparisons between the different groups in the group file. This can be useful if you aren't interested in generating collector's or rarefaction curves for your multi-sample data analysis. It would be worth your while, however, to look at the collector's curves for the calculators you are interested in to determine how sensitive the values are to sampling. If the values are not sensitive to sampling, then you can trust the values. Otherwise, you need to keep sampling. For calc parameter choices see: https://www.mothur.org/wiki/Calculators