# merge.otus

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, constaxonomy_file and a list, shared or relabund file.

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


## Options

### label

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.

### taxlevel

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

## Revisions

• 1.42.0 - First Introduced #558