Shannon Diversity at the gene level

Question

[Bio_Crap]

Hi all, I am trying to calculate Shannon diversity of resistome and stay confused right now. Is usearch the right tool to use? I think it is able to calculate alpha diversity. Is there a huge difference between usearch and vegan package in terms of calculating Shannon diversity?

[MSRS]

Ideally, there should not any huge difference between usearch and vegan package in terms of calculating Shannon diversity. But carefully check your data. You should give your data clearly to answer such a question.

Answer 1

[Joe]

If you have the alignments, you could do something like this to calculate it yourself: https://github.com/jrjhealey/bioinfo-tools/blob/master/Shannon.py