Ncbi Python Packages

eutils

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

gget

🧬 gget enables efficient querying of genomic reference databases

genomepy

genes and genomes at your fingertips

pubmed-search-mcp

🔬 Professional MCP server for biomedical literature research — 40 tools, multi-source search (PubMed, Europe PMC, CORE, OpenAlex), full-text access, citation networks, PICO analysis, and more

ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

pmidcite

Get citation counts for a PubMed paper from the command line

pypubmed

Toolkits for NCBI Pubmed

multitax

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

http-stream-xml

Parse HTTP response as stream, by chunks. Example for NCBI (PubMed) Entrez.

taxadb

:hatching_chick: locally query the ncbi taxonomy

medirect

Multithreaded ncbi edirect and ftract

clinvar-this

ClinVar Submission API Made Easy

taxidtools

A Python Toolkit for Taxonomy

pubmed2

search pubmeds quickly

elastic-blast

ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective

pubmedpy

Utilities for interacting with NCBI EUtilities relating to PubMed

ncbi-submit

A tool to prepare files and run/monitor programmatic submissions to NCBI

taxonomy-ranks

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

ncbitax2lin

🐞 Convert NCBI taxonomy dump into lineages

pyncbi

A Python API library for exploration and data retrieval from NCBI

makura

NCBI Genome downloader

genome-collector

:stars: Easily download genomes and build BLAST/Bowtie indexes in Python

bioinformatics-mcp-server

MCP server for bioinformatics data — genes, proteins, PubMed, ClinVar and sequences via NCBI & UniProt (free, no API key)

orthoevol

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵