Hi All,
I have run the dist.shared command on a data having samples from two places. Sample A has 7728 sequences and sample B has 15473 sequences initially. After various steps I ran the distance command as I wanted to get the bray curtis dissimilarity index. The output of dist.shared command is :
label Group numOtus Otu0001 Otu0002 Otu0003
unique A 7425 1 1 1…
unique B 7425 0 0 0…

I am confused why the number of OTUs is same in both the cases, if the number of sequences are different.

The 7425 is the total number of OTUs in both samples together. If you run summary.single(shared=dist.shared, calc=sobs) you’ll get the number of OTUs in each sample.