Question on agglomerating OTUs by taxonomic rank

[RiboRings]

Hi!

I recently started learning mothur and I am testing its functionality using an OTU dataset that I exported from Bioconductor mia (here 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). 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!

[RiboRings]

This is an example dataset I am using:
example.zip

[pschloss]

Hi - thanks for your question. Would you mind posting this on our forum at forum.mothur.org?

…

On Fri, Apr 24, 2026 at 5:01 AM Giulio Benedetti ***@***.***> wrote: *RiboRings* created an issue (mothur/mothur.github.io#142) <#142> 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! — Reply to this email directly, view it on GitHub <#142>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJUUBBSYF3ILV5AO4I6GPD4XMUNDAVCNFSM6AAAAACYE5CLGSVHI2DSMVQWIX3LMV43ASLTON2WKOZUGMZDCOBRGU4DSOA> . Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS <https://github.com/notifications/mobile/ios/AAJUUBDGOSTAOAETKU5HZQL4XMUNDA5CNFSL4Z3JMQ5C6L3HNF2C22DVMIXUS43TOVSS6NBTGIYTQMJVHA4TRJTSMVQXG33OVJZXKYTTMNZGSYTFMSSWK5TFNZ2KUZTPN52GK4S7NFXXG> and Android <https://github.com/notifications/mobile/android/AAJUUBEOGIVMVGXLHRU5S5L4XMUNDA5CNFSL4Z3JMQ5C6L3HNF2C22DVMIXUS43TOVSS6NBTGIYTQMJVHA4TRJTSMVQXG33OVJZXKYTTMNZGSYTFMSSWK5TFNZ2K4ZTPN52GK4S7MFXGI4TPNFSA>. Download it today! You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[RiboRings]

Sure, thanks for redirecting me!