shannon entropy

[Nicholas_Bokulich]

@Sue

what qiime2 apply in this case ?

See here:

alpha diversity analysis in qiime2 or in R

Hello Nengi, Welcome to the forums! Both packages should work well for calculating alpha diversity values! Under the hood, Qiime2 uses scikit-bio diversity to calculate different alpha values, and Phyloseq uses Vegan. Note that there are some differences in the implementation, like the base of the log used to calculate Shannon diversity. R / Vegan / Phyloseq uses natural log (base e) while Python / Scikit Bio / Qiime uses log2 (base 2). As I write this, Phyloseq should not…

@Sue

Can the animal species and the country where it is raised affect the values?

I would assume so, yes.

Good luck!