Category: classifying

RDP Classifier Updated (Again!)

In August 2023 the RDP Classifier was updated to version 2.14 using bacterial and archaeal training set No. 19. This training set includes 600 new genera and 2,500 new species over the previous version released in 2020, as well as numerous taxonomic rearrangements and adoption of new phyla names as proposed in Oren and Garrity (2021).  For further details, see the release notes.

You may download the updated classifier from Sourceforge. In addition, there are species rank and QIIME2 formatted versions of the training data.

The web version of the RDP Classifier is no longer available.

Reference

Oren, A. and G.M. Garrity. 2021. 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.

RDP Classifier Updated

The RDP Classifier was updated to version 2.13 and released 30 July 2020 on SourceForge (https://sourceforge.net/projects/rdp-classifier/). The update is based on  bacterial and archaeal training set No.18 with over 800 new genera and significant rearrangements of several phyla and genera based on the latest genome analyses.  For detailed explanations of these revisions, please see the release notes.

As in earlier editions, databases are also included for classification of  fungal ITS sequences by UNITE and Warcup taxonomies and for  classification of fungal 28S rRNA gene sequences.

Web Version

The web version of the classifier has been updated to use training set No. 18. The taxonomy browser has also been updated to comply with the new training set.

Installing as a stand-alone application

Written in Java, the RDP Classifier may be installed and run in Windows, Mac OS, Linux, Unix and Solaris environments.

  1. Test if the Java Runtime Environment (JRE) is already installed by opening a terminal and entering:
 java -version
  1. If necessary, install JRE  downloaded from here. While Oracle now charges for the development version of Java (JDK), JRE is still free.
  2. Download RDP Classifier version 2.13 from here and extract the compressed file.

The classifier.jar file will be in sub-directory dist.

Installing as part of RDPTools

The only way to update the classifier in RDPTools is to remove and re-install RDPTools following the instructions here. Updating RDPTools will not work because the new databases are not part of the code but are downloaded during RDPTools installation.

Updating the QIIME2 version of the RDP Classifier

Reference sequences and corresponding taxonomy file for re-training the RDP Classifier included in QIIME2 can be downloaded by clicking here. See this page for how to re-train the classifier.