I am looking to find the order in which OTUs are placed n the *.shared file that is created after performing the read.otu() command for multiple samples. I would like to imput the raw abundances of shared OTUs across each group at a particular cutoff distance into Primer-6. My main trouble is correlating the taxonomy for a particular OTU given by classify.otu() with its location in the *.shared file. Is this possible?
I could just import the Bray-Curtis or Jaccard matrix into Primer-6 directly, although there are some functionalities in that program that I would like to implement prior to the creation of the similarity matrix. Any help would be greatly appreciated!