How to calculate alpha beta diversity

Hi @fbeghini
Is it possible to calculate the alpha-beta diversity analyses using the metaphlan3 pipeline? If yes how I can I do so?


Hi Saraswati,
No, MetaPhlAn does not include a script for alpha diversity calculation. Iā€™d suggest you to check some R packages like vegan or phyloseq.

On a related note, how can you use MetaPhlAn data to calculate alpha diversity since it is marker based not read based?



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Thanks @Sarah_Highlander for putting it very straightforward.

You can treat species like OTUs. alpha.div from rbiom ( can take a species x sample dataframe and estimate several indexes.


Thank you! How would you recommend to rarefy a typical mpa output table with relab using this tool? And which diversity measures do you recommend?

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@fbeghini which diversity measures do you recommend for relative abundances from rbiom? And how do you deal with varying sequencing depth?
All the best,