Can the fasta input file for classify.seqs() be from the sequence alignment (with “.” and “-” characters)??

It runs, but…does the classifier know to ignore the alignment characters?

Yup, it’s smart like that.

Ah. Mothur knows best.

How do I get the classification of the OTUs which are shared between groups? For example, I have 19 OTUs shared by all 6 of my groups, and I want to know what they are (I’m guessing bifidobacteria and some firmicutes…)

It seems like all the info is there, but is there a simple command for getting that?

Try this 2 command combo:

-get.sharedotu(list=your.list, label=OTUdistance, shared=groups-you-want-shared-otu-info, fasta=your.fasta(providing this will give an output of the shared otu sequences))
-classify.seqs(fasta=getsharedotu_output.fasta, template=…, taxonomy=…)

I think that is the best way to do it.



Hi Ryan,

That’s a great suggestion…it worked.