# alpha diversity analysis in qiime2 or in R

**URL:** https://forum.qiime2.org/t/alpha-diversity-analysis-in-qiime2-or-in-r/22270
**Category:** General Discussion
**Created:** [February 23, 2022, 11:17am UTC](https://forum.qiime2.org/t/alpha-diversity-analysis-in-qiime2-or-in-r/22270 "2022-02-23T11:17:55Z")
**Posts on this page:** 1
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### Author: ![colinbrislawn](https://forum.qiime2.org/user_avatar/forum.qiime2.org/colinbrislawn/32/6221_2.png) [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [February 26, 2022, 8:24pm UTC](https://forum.qiime2.org/t/alpha-diversity-analysis-in-qiime2-or-in-r/22270/3 "2022-02-26T20:24:45Z")

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Hello Nengi,

Welcome to the forums! :qiime2:

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](https://github.com/vegandevs/vegan).

Note that there are some differences in the implementation, like the [base of the log used to calculate Shannon diversity](https://forum.qiime2.org/t/shannon-index-value/11649/4). R / Vegan / Phyloseq uses natural log (base e) while Python / Scikit Bio / Qiime uses log2 (base 2).

⚠ **As I write this, Phyloseq should not be used for calculating phylogenetic BETA diversity values** , as there is an [outstanding bug](https://github.com/joey711/phyloseq/issues/956) with how it calculates UniFrac distances.

👍 But the alpha values are fine either way.

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