PyRank

Taxonomy Python Packages

Python packages with the GitHub topic taxonomy. Sorted by relevance, with stars and monthly downloads.
Imageomics
pybioclip

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

9K 63 14
sequana
sequana

Sequana: a set of Snakemake NGS pipelines

3K 151 27
althonos
pyfastani

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

3K 24 2
widdowquinn
pyani

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

3K 218 57
antonheitz
xbrl-forge

Open Source iXBRL Report, xBRL Report and xBRL Taxonomy Generator

2K 8 2
PnX-SI
taxhub

Application de gestion des taxons

2K 27 39
profjsb
tdtax

Open, versioned taxonomy for astronomical time-series sources

2K 12 9
Ecogenomics
gtdbtk

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

2K 613 99
Changwanseo
funvip

Fungal Validation & Identification Pipeline

2K 15 0
althonos
pyskani

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

2K 29 2
lverweijen
littletree

Tree data structure

2K 4 0
gem
openquake-gem-taxonomy-data

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

1K 1 0
HadrienG
taxadb

:hatching_chick: locally query the ncbi taxonomy

980 39 15
pirovc
multitax

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

715 51 4
Changwanseo
genmine

GenBank Record downloader for taxonomists

685 8 0
saezlab
omnipath-client

Python client for the new OmniPath web APIs

642 0 0
gem
openquake-gem-taxonomy

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

612 2 1
moshi4
aniclustermap

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

554 95 12
saezlab
omnipath-utils

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

502 0 0
linzhi2013
taxonomy-ranks

To get taxonomy ranks information with ETE3 from NCBI Taxonomy database.

498 9 4
pyinat
naturtag

Tag your nature photos with iNat taxonomy and observation metadata

464 53 3
ggonnella
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.

462 4 0
zyxue
ncbitax2lin

A tool that converts NCBI taxonomy dump into lineages

431 154 31
smdabdoub
kraken-biom

Create BIOM-format tables from Kraken output.

376 61 16