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.
unipept-visualizations
📊 Unipept visualisations, packaged for easy reusability
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
rtaxref
:package: R client to the API of French Taxonomical Reference (TAXREF)
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.
phageproteomictree
The phage proteomic tree was a breakthrough in evolution, taxonomy, and phylogenetics ... but nobody realized its global importance
letsrept
letsRept is an R package to sample reptile species information from The Reptile Database website
bioclip
This is the repository for the BioCLIP model and the TreeOfLife-10M dataset [CVPR'24 Oral, Best Student Paper].
zetahunter
Reproducible taxonomic classification for Zetaproteobacteria and other poorly resolved taxa.
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"
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.
dfg-fachsystematik-ontology
DFG Fachsystematik Ontology - DFG Classification of Scientific Disciplines, Research Areas, Review Boards and Subject Areas
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.
