Consensus taxonomy of OTUs broken down per group?


I expect this is a very basic question (I’m somewhat of a beginner with Mothur, and with sequence analysis in general), but something I’ve been struggling to work out how to do/if it’s even possible.

I would like to use the consensus taxonomy information outputted by classify.otu to generate a file that lists how many sequences were assigned to each consensus per group.
In other words, I am aiming to create a file similar to the .shared file outputted by make.shared, but with consensus taxonomy information listed in the first column instead of OTU numbers.

Is this possible, and if so, how would I go about generating such a file?


Welcome to the mothur community! Here’s a link to the classify.otu command wiki page, You will want to include your group or count file and set the persample parameter=t.

mothur > classify.otu(, name=final.names, taxonomy=final.taxonomy, label=0.03, persample=t, group=final.groups)

mothur will create a *.cons.taxonomy and *.tax.summary file for each group as well as for the entire dataset.


Hi Sarah,

Thanks for that. Exactly what I’ve been looking for.