RDP Classifier / News: Recent posts

The Bacteria and Archaea hierarchy model used by RDP Classifier has been updated to training set No. 19. The new version has over 600 new genera and 2500 new species added since last version No. 18 released in July 2020. The information that is used to update the RDP taxonomy to training set version No. 19, and RDP Classifier version 2.14 came from publicly available scientific articles and public sequence repository, mostly from International Journal of Systematic and Evolutionary Microbiology (IJSEM), the All-Species Living Tree Project (LTP) and GenBank. ... read more

The Bacteria and Archaea hierarchy model used by RDP Classifier has been updated to training set No. 18. The new version has over 800 new genera and 4000 new species added. Major rearrangements for Classifier training set No. 18 include the following:

1. The class Alphaproteobacteria has been rearranged based on genome data ( Hördt A, et al. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol. 2020;11:468. doi:10.3389/fmicb.2020.00468).... read more

The Fungal LSU hierarchy model used by RDP Classifier has been updated to training set No. 11. The new Fungal LSU training set offers increased coverage of the Glomeromycota, Chytridiomycota and other basal lineages, with expanded non-fungal Eukarya phyla to better separate fungi from other eukaryotes.

The RDP Classifier is a naïve Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. More information can be found at http://rdp.cme.msu.edu/.

Environmental gene library analysis has become a mainstream tool in microbial ecology due to the rapid improvements in high-throughput sequencing technology. The small-subunit rRNA gene is often targeted for library construction because of its uses as a phylogenetic marker and in bacterial identification. However, tools for simple and rapid identification of the large numbers of sequences have been lacking. Here we present a naïve Bayesian classifier (RDP Classifier) which can rapidly and accurately classify bacterial 16s rRNA sequences into the new higher-order taxonomy proposed by Bergey’s Trust. It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. The RDP Classifier is suitable both for analysis of single rRNA sequences and for analysis of libraries of thousands of sequences. This Classifier is fast, does not require sequence alignment and works well with partial sequences.... read more