What is command (qiime 1.7) for beta diverse if I do not have rep_set.tre

[Muhammad Umar Sohail]

Dear fellows

I hope you are all doing great. I use qiime 1.7. I do not have rep_set.tre file. I want to get beta diverse with plots for pcoa plots.
Please suggest a command for this pirpose.

[Colin Brislawn]

Hello Muhammad,

What method of OTU picking did you use to make your rep_set.fna file? If you use closed-ref, you can use the green genes .tre file with the beta diversity scripts. If you use open-ref OTU picking, a tree file should have been created along with your rep_set.fna file.

You could also use a beta diversity distance metric that does not need a .tre file. For example, you could use -m euclidean.

I hope that helps!

Colin