Fastsubtrees
Fastsubtrees: simple and efficient subtrees extractions in Python with applications to NCBI taxonomy - Published in JOSS (2022)
treemaker
treemaker: A Python tool for constructing a Newick formatted tree from a set of classifications. - Published in JOSS (2018)
Taxonomy Resolver
Taxonomy Resolver: A Python package for building and filtering taxonomy trees - Published in JOSS (2025)
pyskani
PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.
pyfastani
Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
gtdbtk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
finbif
R interface for the Finnish Biodiversity Information Facility (FinBIF) API
pyani
Application and Python module for average nucleotide identity analyses of microbes.
typetaxonscript
Build a resilient biotaxonomic database through collaborative efforts, ensuring endurance and minimizing redundancy
taxtriage
TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomic NGS data. This flexible tool was developed with various use-cases of mNGS in mind.
dada2
Accurate sample inference from amplicon data with single nucleotide resolution
gbif.range
An R package to generate species range maps based on ecoregions and a user-friendly GBIF wrapper
technology-carbon-standard
An emerging unifying standard for understanding, quantifying, and reducing carbon emissions from an organisation's technology landscape. A component of a holistic Technology Sustainability Framework.
https://github.com/broadinstitute/vectreeid
Amplicon taxonomic identification pipeline for Neafsey Lab
aniclustermap
A tool for drawing ANI clustermap between all-vs-all microbial genomes
kraken-biom
Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
taxonomy4good
Taxonomy4Good: a sustainability lexicon that provides the freedom to create custom taxonomies in addition to listed ESG and Sustainability Standards taxonomies.
ornithophile
🦜 Ornithophile is a powerful and elegant REST API providing detailed data on 11,290 bird species, including taxonomy, images, conservation status, and alphabetical filtering. Ideal for nature lovers, developers, and researchers.
unifesp_ntm_newspecies-nf
Paper "Description of new species of Mycobacterium terrae complex isolated from sewage at the São Paulo Zoological Park Foundation in Brazil"
bioclip
This is the repository for the BioCLIP model and the TreeOfLife-10M dataset [CVPR'24 Oral, Best Student Paper].
dfg-fachsystematik-ontology
DFG Fachsystematik Ontology - DFG Classification of Scientific Disciplines, Research Areas, Review Boards and Subject Areas
letsrept
letsRept is an R package to sample reptile species information from The Reptile Database website
phageproteomictree
The phage proteomic tree was a breakthrough in evolution, taxonomy, and phylogenetics ... but nobody realized its global importance
https://github.com/boniolp/tsadtaxonomy
This application helps users explore and understand the vast array of existing methods, ranging from traditional statistical approaches to modern machine learning algorithms. It visualizes a structured, process-centric taxonomy of anomaly detection techniques, enabling a deeper insight into the research landscape.
zetahunter
Reproducible taxonomic classification for Zetaproteobacteria and other poorly resolved taxa.