Taxonomy Python Packages

sequana

Sequana: a set of Snakemake NGS pipelines

pyfastani

Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.

pybioclip

Python package and CLI that simplifies using the BioCLIP family of foundation models.

funvip

Fungal Validation and Identification Pipeline

pyskani

PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.

taxhub

Application web de gestion centralisée des taxons basée sur le référentiel TAXREF

xbrl-forge

Generate XBRL Instances, iXBRL instances, xBRL Taxonomies and xBRL extension taxonomies from distributed sources

littletree

Tree data structure

gtdbtk

A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

pyani

Application and Python module for average nucleotide identity analyses of microbes.

omnipath-client

Python client for the new OmniPath web APIs

multitax

A Python package for obtaining, parsing and exploring biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)

genmine

GenBank Record downloader for taxonomists

taxadb

:hatching_chick: locally query the ncbi taxonomy

tdtax

Open, versioned taxonomy for astronomical time-series sources

openquake-gem-taxonomy-data

Openquake Gem Building Taxonomy Data - GEM building taxonomy data and python classes to access it.

joltax

JolTax is a high-performance, vectorized taxonomy library for Python.

taxidtools

A Python Toolkit for Taxonomy

omnipath-utils

Prior-knowledge processing utilities Python package, database and web API

aniclustermap

A tool for drawing ANI clustermap between all-vs-all microbial genomes

naturtag

Tag your nature photos with iNat taxonomy and observation metadata

taxonomy-ranks

To get taxonomy ranks information with ETE3 Python3 module (http://etetoolkit.org/)

ncbitax2lin

🐞 Convert NCBI taxonomy dump into lineages

world-of-taxanomy

1,000+ open taxonomy systems with 1.2M+ codes and 320K+ crosswalk edges. NAICS, ISIC, NACE, HS, SOC, ISCO, ESCO, CPC, UNSPSC, ICD-10/11, Patent CPC, GDPR, and more - all connected. REST API + MCP server for AI agents. Open source (MIT) by Colaberry Inc.