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Shannon Diversity at the gene level

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?

shannon diversity alpha
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updated by Joe Joe • written by Bio_Crap • Bio_Crap

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.

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written by MSRS MSRS

1 answer

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

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written by Joe Joe

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