Dear all,
While performing my data analysis I used the Greengenes nomenclature (silva.bacteria.gg.tax) with the SILVA sequences provided in the SILVA bacterial package. It seems there is an inconsistency with other nomenclatures (beta-Proteobacteria are provided as a subdivision of the gamma-proteobacterial class). Maybe this is something to investigate or provide related information about.
Some examples of the file are the following:
AF515816.1 Bacteria;Proteobacteria;Gammaproteobacteria;Betaproteobacteria;Rhodocyclales;Azoarcus;BANW526;
AY212590.1 Bacteria;Proteobacteria;Gammaproteobacteria;Betaproteobacteria;Comamonadaceae;Unclassified;
AJ534663.1 Bacteria;Proteobacteria;Gammaproteobacteria;Betaproteobacteria;Rhodocyclales;Azospira;
AJ544690.1 Bacteria;Proteobacteria;Gammaproteobacteria;Betaproteobacteria;Burkholderiaceae;Unclassified;
AF170351.1 Bacteria;Proteobacteria;Gammaproteobacteria;Betaproteobacteria;Rhodocyclales;Azospira;
AY353696.1 Bacteria;Proteobacteria;Gammaproteobacteria;Betaproteobacteria;Burkholderiaceae;Unclassified;
AY486373.1 Bacteria;Proteobacteria;Gammaproteobacteria;Betaproteobacteria;Burkholderiaceae;Burkholderia_cepacia_complex;Burkholderia_cepacia;
AB021331.1 Bacteria;Proteobacteria;Gammaproteobacteria;Betaproteobacteria;Comamonadaceae;Comamonas;Unclassified;
AB166780.1 Bacteria;Proteobacteria;Gammaproteobacteria;Betaproteobacteria;Comamonadaceae;Comamonas;Acidovorax;bacterium_rJ12;bacterium_rM4;
Best regards,
Sotirios