Is there a built in way to tell mother to classify the different taxonomic levels with individual cutoff values using the classify.seqs command? For instance I want to classify genus at 97% similarity, Family at 90% and order at 80%. I can do them all separately with three versions of the taxonomy file, but since you can classify at three levels it makes sense to be able to impose different cutoff values for each level too, I think.
Thanks!
Wendy
Hi Wendy,
You can certainly generate OTUs at each of those thresholds using the cluster command and a large enough cutoff. However, if you want genus, family, etc. level names, you should really just use the phylotype command. There is really no support for mapping thresholds to taxonomic levels since the diversity within each level varies so much.
Pat