How to calculate pure compositional distance in QIIME?

[Cloud. Li]

Hi everyone,

I have got an OTU table and want to calculate pure compositional distance for each sample pair. That means no OTU abundance and no phylogenetic structure being considered. Is there a metric in beta_diversity.py able to do this?

[Kyle Bittinger]

No, you have to do this yourself.  I recommend exporting the table to tsv format using "biom convert".

What specific transformation will you use (alr, clr, etc) and how will you deal with zeros in your data?

Best,

Kyle