I was wondering if mothur has a command that lets you know sequence similarity thresholds for the phylotype command; that is, if default (species level) is 97% sequence similarity for a single OTU, which is this threshold for genus, family, order, class and phyla?
Any clues would be greatly appreciated.
We really need to get away from this idea that there’s a mapping between % similarity and taxonomic levels. If you want a genus, family, etc. then use the phylotype command. If you want a sub-genus taxonomic level use OTUs at an 0.03 cutoff. We dealt with this a bit in Fig 2A of Westcott & Schloss 2011:
You’ll see broad divergence for each taxonomic level which basically says there is no single distance-based cutoff that works for each taxonomic level.