Updated RDP taxonomy and RDP Classifier for more accurate taxonomic classification

Updated RDP taxonomy and RDP Classifier for more accurate taxonomic classification

April 2024 | Qiong Wang, James R. Cole
The RDP Classifier, a widely used machine learning tool for taxonomic classification, has been updated along with the RDP taxonomy to improve accuracy. The RDP taxonomy, based on validly named species and higher taxonomic ranks, has been updated to training set No. 19, incorporating newly described taxa and recent changes in prokaryotic nomenclature. This update includes 24,642 sequences from 19,074 species and 3,903 genera, representing a 13.8% and 20.6% increase compared to the previous version. The update includes thousands of taxonomic changes and name revisions, many based on newly valid phylum names. The RDP Classifier has also been updated to version 2.14 with numerous enhancements and bug fixes. Notable features include cross-validation testing, which helps users train the classifier with their own data and identify misclassified sequences. Another enhancement allows users to adjust taxon assignment counts based on 16S gene copy number information. The RDP taxonomy was updated using the International Journal of Systematic and Evolutionary Microbiology, the List of Prokaryotic names with Standing in Nomenclature, and public sequence repositories. The RDP Classifier is highly cited and remains a valuable tool in microbiome studies. The updated RDP taxonomy and Classifier are available for download, along with instructions for installation and use. The authors declare no conflict of interest.The RDP Classifier, a widely used machine learning tool for taxonomic classification, has been updated along with the RDP taxonomy to improve accuracy. The RDP taxonomy, based on validly named species and higher taxonomic ranks, has been updated to training set No. 19, incorporating newly described taxa and recent changes in prokaryotic nomenclature. This update includes 24,642 sequences from 19,074 species and 3,903 genera, representing a 13.8% and 20.6% increase compared to the previous version. The update includes thousands of taxonomic changes and name revisions, many based on newly valid phylum names. The RDP Classifier has also been updated to version 2.14 with numerous enhancements and bug fixes. Notable features include cross-validation testing, which helps users train the classifier with their own data and identify misclassified sequences. Another enhancement allows users to adjust taxon assignment counts based on 16S gene copy number information. The RDP taxonomy was updated using the International Journal of Systematic and Evolutionary Microbiology, the List of Prokaryotic names with Standing in Nomenclature, and public sequence repositories. The RDP Classifier is highly cited and remains a valuable tool in microbiome studies. The updated RDP taxonomy and Classifier are available for download, along with instructions for installation and use. The authors declare no conflict of interest.
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