RDP Classifier 2.14 (August 2023) Released

Qiong Wang — Wed, 23 Aug 2023 21:03:15 -0000

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.

It is worth noting that most of the phyla have new names, according to article "
Oren A, Garrity GM. Valid publication of the names of forty-two phyla of prokaryotes. Int J Syst Evol Microbiol. 2021 Oct;71(10). doi: 10.1099/ijsem.0.005056. PMID: 34694987."

In addition to the files to train and run the RDP Classifier, new file formats are made available to accommodate the needs of users:

A new file trainset19_072023_speciesrank.fa has been added to the release in RDPClassifier_16S_trainsetNo19_rawtrainingdata.zip. This file is NOT needed to train the classifier. In addition to sequences, it contains genus, species, strain, type status and taxonomy rank, which are useful for closest species identification using third-party tools (e.g. BLAST).
Two new files in RDPClassifier_16S_trainsetNo19_QiimeFormat.zip to retrain the RDP Classifier included in Qiime2 package.

For suggestions and feedback, please contact:
Qiong Wang wangqion@gmail.com or qiong.wang@iff.com
James Cole colej@msu.edu

RDP Classifier 2.13 (July 2020) Released

Qiong Wang — Fri, 24 Jul 2020 18:39:20 -0000

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:

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).
Part of the class Gammaproteobacteria has been rearranged based on genome data (Spring S, et al.. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Front Microbiol. 2015;6:281. doi:10.3389/fmicb.2015.00281).
The former class Epsilonproteobacteria is moved to a new phylum and renamed as Campylobacterota ( Waite DW, et al. Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.) [published correction appears in Front Microbiol. 2018 Apr 18;9:772]. Front Microbiol. 2017;8:682. doi:10.3389/fmicb.2017.00682).
The phylum Bacteroidetes has been rearranged based on genome data (García-López M, et al. Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Front Microbiol. 2019;10:2083. doi:10.3389/fmicb.2019.02083).
The phylum Actinobacteria has been rearranged based on genome data (Nouioui I, et al. Genome-Based Taxonomic Classification of the Phylum Actinobacteria. Front Microbiol. 2018;9:2007. doi:10.3389/fmicb.2018.02007)
The phylum Tenericutes has been rearranged based on genome data (Gupta RS, et al. Phylogenetic framework for the phylum Tenericutes based on genome sequence data: proposal for the creation of a new order Mycoplasmoidales ord. nov., containing two new families Mycoplasmoidaceae fam. nov. and Metamycoplasmataceae fam. nov. harbouring Eperythrozoon, Ureaplasma and five novel genera [published correction appears in Antonie Van Leeuwenhoek. 2018 Dec;111(12):2485-2486]. Antonie Van Leeuwenhoek. 2018;111(9):1583-1630. doi:10.1007/s10482-018-1047-3)
Several species from genus Bacillus has been transferred into 6 novel genera based on comparative genomic analyses of Bacillus species (Patel S, Gupta RS. A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. Int J Syst Evol Microbiol. 2020;70(1):406-438. doi:10.1099/ijsem.0.003775)
The genus Lactobacillus has been reclassified into 25 genera based on genome data ( Zheng J, et al. A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. Int J Syst Evol Microbiol. 2020;70(4):2782-2858. doi:10.1099/ijsem.0.004107).

In addition to the two files to train the RDP Classifier, new file formats are made available to accommodate the needs of users:

A new file trainset18_062020_speciesrank.fa has been added to the release in RDPClassifier_16S_trainsetNo18_rawtrainingdata. This file is NOT needed to train the classifier. In addition to sequences, it contains genus, species, strain, type status and taxonomy rank, which are useful for closest-species identification using third-party tools (e.g. BLAST).
Two new files in RDPClassifier_16S_trainsetNo18_QiimeFormat to retrain the RDP Classifier included in Qiime2.

RDP Classifier 2.7 released with updated Fungal LSU training set

Qiong Wang — Wed, 12 Mar 2014 16:12:27 -0000

The Fungal LSU hierarchy model used by RDP Classifier and RDP Hierarchy Browser 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.

RDP Classifier 1.0 released

Qiong Wang — Thu, 30 Nov 2006 17:01:23 -0000

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.

The Classifier and related software were written in Java (API v1.4.1) and have been tested on the Solaris (2.8), Linux (2.4.23) and Macintosh (OS 10.3) operating systems using Java virtual machines from Sun and Apple.

The compiled RDP Classifier library includes the data from Bergey's bacterial taxonomy outline release 5.0 as the default trained data. To run the Classifier with the default settings, simply provide a file with one or more bacterial 16S rRNA sequences in FASTA, Genbank or EMBL format. The classification results will be written to an output file.

The RDP Classifier is not limited to using the bacterial taxonomy proposed by the Bergey's editors. It worked equally well when trained on the NCBI taxonomy. Two files are needed to train the Classifier: one taxonomy file describing the relationships between the taxa, and another file containing trusted seqeunces, each labeled with taxonomic assignments, from domain to genus level.

To continue improving RDP Classifier, we now need your help in testing them. Please download the package and try to use it. Please contact rdpstaff@msu.edu or (517) 432-4998 if you have any questions or suggestions.

This research was supported by the Office of Science (BER), U.S. Department of Energy, Grant No. DE-FG02-99ER62848 and the National Science Foundation, Grant No. DBI-0328255.

Recent posts to news

RDP Classifier 2.14 (August 2023) Released

RDP Classifier 2.13 (July 2020) Released

RDP Classifier 2.7 released with updated Fungal LSU training set

RDP Classifier 1.0 released