I downloaded the Silvav123 taxonomy file and did a quick bit of unix magic. I noticed that the file does not classify down to species. Is this actually the case? Maybe I will try Silvav128?
My question is, does Silva have a taxonomy file that classifies to species level?
This link shows a " silva.slv.taxonomy" file with a few lines of classification to the species level. How do I get this file?
It is a stretch to think that you can classify a bacterium to the species level based on a 16S rRNA gene sequence or a fragment of the gene. The gene just doesn’t have the resolution for most taxa, the database annotations for species names are pretty poor, and you would need a significantly larger database. This just isn’t possible.
There is no species information in v128 either.