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The merge.otus command will combine OTUs based on taxonomic assignment.

Default Settings

To run the merge.otus command you need to provide consensus taxonomy file, https://mothur.org/wiki/Constaxonomy_file and a list, shared or relabund file.

mothur > merge.otus(constaxonomy=final.opti_mcc.0.03.constaxonomy, list=final.opti_mcc.list)



The label parameter allows you to indicate which labels you want to include, label names should be separated by dashes. Default is all labels in your list file.


The taxlevel parameter allows you to specify the taxonomy level you would like to use when merging. Default=maxlevel.


  • 1.42.0 - First Introduced #558