dist.shared

Commands in mothur
1

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.
2

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.