RDP Classifier

If you're looking for a rapid and accurate way to classify bacterial 16s rRNA sequences into the new higher-order taxonomy proposed by Bergey's Trust, then RDP Classifier is the software you need. Developed as a naive Bayesian classifier, it uses rRNA sequence data to provide taxonomic placement, with taxonomic assignments provided from domain to genus, including confidence estimates for each assignment.

One of the best things about the RDP Classifier is that it's not limited to using the bacterial taxonomy proposed by the Bergey's editors. In fact, it worked equally well when trained on the NCBI taxonomy, meaning it's incredibly versatile and adaptable. You could even use it to adapt to additional phylogenetically coherent bacterial taxonomies.

Using the RDP Classifier means that you can easily assign 16S rRNA gene sequences to the new phylogenetically consistent higher-order bacterial taxonomy proposed by Garrity et al. The hierarchical taxa are based on a naive Bayesian rRNA classifier, making it a reliable, robust and accurate tool suitable for scientific research and analyses. The newly trained classifier even allows classification of both bacterial and archaeal 16S rRNA sequences, making it an inclusive and all-encompassing piece of software.