Taxonomy Python Packages

ontodag

Associative memory and categories based on a directed acyclic graph data structure

pybioclip

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

tdtax

Open, versioned taxonomy for astronomical time-series sources

pyfastani

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

pyskani

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

funvip

Fungal Validation and Identification Pipeline

sequana

Sequana: a set of Snakemake NGS pipelines

stapel-vocabularies

Reference vocabularies (levels, terms, edges) behind stapel-attributes' ref_select types, for the Stapel framework

django-icv-taxonomy

Taxonomy, vocabularies, and tagging for Django: term trees, generic tagging, and SKOS-style relationships

pyani

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

taxomesh

A multi-parent category graph with a Python stdlib-style interface — subscript, get, in, len, del — over YAML, JSON or Django storage.

figtreekit

Programmatic styling of phylogenetic trees for FigTree visualization

gtdbtk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

taxhub

Application de gestion des taxons

openquake-gem-taxonomy-data

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

xbrl-forge

Open Source iXBRL Report, xBRL Report and xBRL Taxonomy Generator

openquake-gem-taxonomy

Openquake Gem Taxonomy - python package to manage GEM building taxonomy strings.

littletree

Tree data structure

multitax

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

taxadb

:hatching_chick: locally query the ncbi taxonomy

aspect-data

⛰️ Serializable featurization pipelines for ML/AI on chemistry, taxonomy, and general tabular data.

genmine

GenBank Record downloader for taxonomists

taxidtools

Python library to deal with taxonomic IDs and lineages from the NCBI's Taxdump files

aniclustermap

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