phylotype command Levels thresholds

Hi all

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.

Thanks much


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.