# Agglomerating OTUs by taxonomic rank

**URL:** <https://forum.mothur.org/t/agglomerating-otus-by-taxonomic-rank/22410>\
**Category:** Commands in mothur\
**Created:** [May 1, 2026, 7:59pm UTC](https://forum.mothur.org/t/agglomerating-otus-by-taxonomic-rank/22410 "2026-05-01T19:59:51Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![RiboRings](https://avatars.discourse-cdn.com/v4/letter/r/59ef9b/32.png) [@RiboRings](https://forum.mothur.org/u/RiboRings)\
**Post date:** [May 1, 2026, 7:59pm UTC](https://forum.mothur.org/t/agglomerating-otus-by-taxonomic-rank/22410/1 "2026-05-01T19:59:51Z")

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Hi!

I recently started learning mothur and I am testing its functionality using an OTU dataset that I exported from Bioconductor mia ([here](https://microbiome.github.io/mia/reference/mia-datasets.html) are some examples).

I am currently looking for a function in mothur to agglomerate (sum) OTUs by a specific taxonomic rank (e.g., Family) and return the agglomerated counts table (similar to [mia::agglomerateByRank](https://microbiome.github.io/mia/reference/agglomerate-methods.html)). I spotted the `make.shared`, `tax.summary` and `classify.otu` as potential candidates, but I do not have a list file. What I have is a OTU-level count table, taxonomy, tree and sample metadata.

Could you give me a hint how agglomeration could be done in mothur?

Thanks in advance!

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**Author:** ![RiboRings](https://avatars.discourse-cdn.com/v4/letter/r/59ef9b/32.png) [@RiboRings](https://forum.mothur.org/u/RiboRings)\
**Post date:** [May 1, 2026, 8:00pm UTC](https://forum.mothur.org/t/agglomerating-otus-by-taxonomic-rank/22410/2 "2026-05-01T20:00:36Z")

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P.S. An example dataset I am using is attached to [this issue](https://github.com/mothur/mothur.github.io/issues/142#issuecomment-4347097034) in GitHub.

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**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\
**Post date:** [May 4, 2026, 1:22pm UTC](https://forum.mothur.org/t/agglomerating-otus-by-taxonomic-rank/22410/3 "2026-05-04T13:22:10Z")

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Hi there,

Thanks for the question. If you have taxonomy data, you can likely reformat it into a mothur format and use our phylotype function and then go from there. The phylotypr function allows you to bin sequences at any taxonomic level. I’d suggest looking at this section of the MiSeq SOP…

> **[Phylotypes - MiSeq SOP](https://mothur.org/wiki/miseq_sop/#phylotypes)**
>
> NOTE: Although this is an SOP, it is something of a work in progress and continues to be modified as we learn more. If you are using this protocol in a paper, you must cite the Schloss et al. 2013 AEM paper and cite the date you accessed this page: |...

Pat

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**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\
**Post date:** [May 14, 2026, 1:22pm UTC](https://forum.mothur.org/t/agglomerating-otus-by-taxonomic-rank/22410/4 "2026-05-14T13:22:25Z")

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