Computational Biology Python Packages

biotite

A comprehensive library for computational molecular biology

scikit-bio

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

cobra

COBRApy is a package for constraint-based modeling of metabolic networks.

biopandas

Working with molecular structures in pandas DataFrames

brisc

Fast single-cell toolkit

glycowork

Package for processing and analyzing glycans and their role in biology.

msasim

Backend C++ code for the Sailfish MSA simulation library using the Pybind11 framework

biosimulators-utils

Utilities for building standardized command-line interfaces for biosimulation software packages

natal-core

Numerical Aggregation Toolkit for Analysis of Lifecycles

myokit

Source code, issues, and discussions for Myokit: A tool for cardiac electrophysiology modelling and simulation

dotmatch

Fast exact short-DNA known-target assignment for CRISPR guides, barcodes, primers, panels, and whitelists.

kisao

Ontology of algorithms for analyzing biological models, their parameters, and their outputs

pertpy

Single-cell perturbation analysis

zombi2

A Python library for simulating the evolution of species, genomes, sequences and traits

lzgraphs

Alignment-free graph models of TCR and BCR repertoires built from Lempel-Ziv and FlashBack string decompositions. Compute sequence generation probability (Pgen) and repertoire diversity, and generate new sequences. Python with a C core.

protspace

Explore protein language model embeddings in your browser — surface relationships sequence similarity misses, overlay annotations, and transfer labels (EAT). Nothing uploaded.

qc-iodata

Python library for reading, writing, and converting computational chemistry file formats and generating input files.

scrna-matrix

High-performance C++ genomics library and Python extension for fast omics processing, sequence analysis, and stream profiling.

protlabel

Explore protein language model embeddings in your browser — surface relationships sequence similarity misses, overlay annotations, and transfer labels (EAT). Nothing uploaded.

brendapyrser

A Python parser for the BRENDA database

indra

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

diffbio

End-to-end differentiable bioinformatics for JAX/Flax NNX: soft Smith-Waterman alignment, read mapping and assembly, variant calling, RNA-seq, single-cell, epigenomics, CRISPR, metabolomics, multi-omics, protein and RNA structure, molecular dynamics and drug-discovery operators composed into trainable pipelines on the Avitai stack.

chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

graphein

Protein Graph Library