Taxonomy Python Packages

pybioclip

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

xbrl-forge

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

sequana

Sequana: a set of Snakemake NGS pipelines

littletree

Tree data structure

taxhub

Application de gestion des taxons

funvip

Fungal Validation and Identification Pipeline

pyani

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

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.

gtdbtk

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

openquake-gem-taxonomy-data

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

tdtax

Open, versioned taxonomy for astronomical time-series sources

openquake-gem-taxonomy

Openquake Gem Taxonomy - Package to manage GEM Building Taxonomy strings

multitax

Python package to obtain, parse and explore biological and custom taxonomies.

taxadb

:hatching_chick: locally query the ncbi taxonomy

omnipath-client

Python client for the new OmniPath web APIs

aniclustermap

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

genmine

GenBank Record downloader for taxonomists

taxidtools

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

naturtag

Tag your nature photos with iNat taxonomy and observation metadata

omnipath-utils

ID translation, taxonomy, orthology and reference lists for molecular biology

ncbitax2lin

A tool that converts NCBI taxonomy dump into lineages

fastsubtrees

Python library and command line script , for fast extraction of subtrees of fairly large trees, consisting of millions of nodes, such as the NCBI taxonomy tree.

kraken-biom

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).