Before I go into writing a script using other tools - does mothur calculate the average distance between OTU/ASVs within sample? I would like to compare that between all my samples (as a rough proxy for phylogenetic diversity - and no, I do not have a reliable tree to place all my data).
I could not find any command I can trick mothur into doing something like that.
The AMOVA/HOMOVA command does it under the hood and outputs the SS/MSE values. Not sure if that’s what you’re looking for. You would need to feed it a distance matrix/design file for sequences rather than samples. I suspect you’ll have to roll your own script, but the AMOVA/HOMOVA literature (Anderson M) is pretty good for describing how to calculate the distances.
thanks - that it what I was afraid. I think AMOVA/HOMOVA would give me more FST distances and alike. I was looking for average distances between ASVs.
Anyway - I did write the script, didn’t take much from the fasta files and the count files, and runs very fast. Might not be elegant, but it works : )