# Remove dominant OTU

**URL:** <https://forum.mothur.org/t/remove-dominant-otu/22400>\
**Category:** Uncategorized\
**Created:** [January 16, 2026, 11:13pm UTC](https://forum.mothur.org/t/remove-dominant-otu/22400 "2026-01-16T23:13:32Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![jbailey](https://avatars.discourse-cdn.com/v4/letter/j/b5a626/32.png) [@jbailey](https://forum.mothur.org/u/jbailey)\
**Post date:** [January 16, 2026, 11:13pm UTC](https://forum.mothur.org/t/remove-dominant-otu/22400/1 "2026-01-16T23:13:32Z")

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I’m analyzing a dataset in which all samples contain the same dominant OTU. I’m curious about comparing the treatments based on the remaining OTUs. After I perform the steps to cluster my samples by OTUs (through classify.OTU), is there a command or series of steps that will allow me to remove a single OTU before I move on to rarefaction and then alpha and beta diversity analyses?

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**Author:** ![leocadio](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/leocadio/32/203_2.png) [@leocadio](https://forum.mothur.org/u/leocadio)\
**Post date:** [January 19, 2026, 11:34pm UTC](https://forum.mothur.org/t/remove-dominant-otu/22400/2 "2026-01-19T23:34:33Z")

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If you know the OTU name - remove.seqs looks straight forward?

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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:** [January 21, 2026, 12:52pm UTC](https://forum.mothur.org/t/remove-dominant-otu/22400/3 "2026-01-21T12:52:49Z")

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Hey - try [remove.otus](https://mothur.org/wiki/remove.otus/)  
Pat