Order of OTUs in Shared file

Hi everyone,
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!


In the .shared file, otu 1 represents the raw abundance of each group in otu 1 of your list file. The output from classify.otu is a three column file. Column 1 is the otu number from the list file. Column 2 is the number of the sequences that the taxonomy represents. If no .names file is used it is the raw abundance of the otu in the list file. Column 3 is the consensus taxonomy. I hope this helps.

Yep, that’s exactly what I was looking for. Thanks!