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Recommended Projects

Free DELTA
Software tools for processing taxonomic descriptions in DELTA format
ParsInsert
ParsInsert efficiently produces both a phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis. This is a C++ implementation of the Parsimonious Insertion algorithm.
Taxallnomy
Taxallnomy is a taxonomic database that provides taxonomic lineages according to the ranks used on Linnean classification system (e.g. Kingdom, Phylum, Class etc.). Taxallnomy is based on the NCBI Taxonomy, thus you will find along the taxonomic lineage either taxa originally ranked in NCBI Taxonomy or some unique nodes created by the Taxallnomy algorithm, since some taxonomic ranks are missing in the original taxonomic lineage (for example, the Superclass rank is missing on the Homo sapiens lineage).
LMAT
Efficient taxonomic labeling of very large metagenomic datasets.
RDP Classifier
The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments for bacterial and archaeal 16S rRNA sequences, fungal LSU and fungal ITS sequences, with confidence estimates for each assignment. More information and tutorials on how to install, use and retrain RDP Clasifier can be found on at https://github.com/rdpstaff/classifier and John Quensen's blog (https://john-quensen.com/). Citation: 1. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007 Aug;73(16):5261-7. 2. Wang Q, Cole JR. Updated RDP taxonomy and RDP Classifier for more accurate taxonomic classification. Microbiol Resour Announc. 2024 Apr 11;13(4):e0106323.