Output of classify.otus

Hi,

My PI was wondering about the meaning of the quotation marks around some taxonomic classifications after running classify.otus:
For example in this below case:

Bacteria(100);“Actinobacteria”(100);Actinobacteria(100);Actinomycetales(100);unclassified(100);unclassified(100);
Bacteria(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);
Bacteria(100);“Proteobacteria”(100);Gammaproteobacteria(100);Pasteurellales(100);Pasteurellaceae(100);unclassified(100);
Bacteria(100);Firmicutes(100);Bacilli(100);Bacillales(100);unclassified(100);unclassified(100);

why are Actinobacteria and Proteobacteria in quotation marks but Firmicutes is not?

Thanks for your help,

Laura

Are they in quotes in the reference files you used?

Yeah, I originally used one of the training sets provided on the mothur website to make my taxonomy file (trainset9_032012.pds.tax) and these contain the same quotes around the same taxonomies.

I’m just not sure if that’s meant to indicate something?

Thanks for your help,

Laura

I believe the quotes mean that the names were never officially proposed.