I’m wanting to just look at one particular taxa, so have selected that linage from my shared file and now have a slop OTU that is orders of magnitude more abundant than any of the OTUs of interest. I can’t think of how to subset including that OTU but then not use that OTU in calculating the sample dissimilarities, yet I feel like that would be better??
Sorry… I’m not sure what you mean. Are you using get.lineage/remove.lineage?