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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.

4K 61 13
antonheitz
xbrl-forge

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

3K 6 2
sequana
sequana

Sequana: a set of Snakemake NGS pipelines

3K 151 27
lverweijen
littletree

Tree data structure

3K 4 0
PnX-SI
taxhub

Application de gestion des taxons

3K 26 38
Changwanseo
funvip

Fungal Validation and Identification Pipeline

3K 14 0
widdowquinn
pyani

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

3K 217 56
althonos
pyfastani

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

3K 24 2
althonos
pyskani

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

2K 29 2
Ecogenomics
gtdbtk

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

2K 598 98
gem
openquake-gem-taxonomy-data

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

2K 1 0
profjsb
tdtax

Open, versioned taxonomy for astronomical time-series sources

1K 12 9
gem
openquake-gem-taxonomy

Openquake Gem Taxonomy - Package to manage GEM Building Taxonomy strings

1K 2 1
pirovc
multitax

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

974 50 4
HadrienG
taxadb

:hatching_chick: locally query the ncbi taxonomy

951 39 15
saezlab
omnipath-client

Python client for the new OmniPath web APIs

621 0 0
moshi4
aniclustermap

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

616 93 12
Changwanseo
genmine

GenBank Record downloader for taxonomists

596 8 0
CVUA-RRW
taxidtools

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

497 3 2
pyinat
naturtag

Tag your nature photos with iNat taxonomy and observation metadata

450 53 3
saezlab
omnipath-utils

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

436 0 0
zyxue
ncbitax2lin

A tool that converts NCBI taxonomy dump into lineages

399 153 31
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.

388 4 0
smdabdoub
kraken-biom

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

324 61 16
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