I am trying to run the get.sharedseqs command in Mothur. Everytime I run the get.sharedseqs command Mothur tells me that there are no shared otus at distance of 0.01, 0.02, 0.03, 0.04 etc. However, the get.oturep command groups produces OTUs at these same distances. I am not sure where I am making an error. I used the column distance matrix format. To run the get.sharedseqs command I input the fn.list file, the groups file, the label values I am interested in, and i specify an output using shared= . Hopefully this makes sense. Any help would be appreciated.