Different Shannon diversity results between QIIME2 and phyloseq

[Nicholas_Bokulich]

Hi @Felipe_Rocha,
Please see here:

shannon index value

Hello Ana, A bunch of things can affect the Shannon index. Switching from OTUs to ASVs can change it. The Shannon index uses a log scale, but it can use log2 or log10 or natural log, and all of these are perfectly valid nobody EVER reports which one they are using! This sounds crazy. And it is. And yet if you look in the original Shannon entropy paper that has 69,200 citations, all three of these log bases are mentioned on page one: The choice of a logarithmi…