Open-source bioinformatics software

119 open-source libraries, tools and applications tagged bioinformatics, ranked by how closely bioinformatics is their primary purpose, then by adoption and maintenance health. Each entry links to a page with sources, use cases and when to choose or avoid it.

119 products, primary matches first, then adoption-weighted; health v2 shown.

Product	Health v2	Stars	Maturity
fiji/fiji Fiji is a batteries-included distribution of ImageJ, bundling thousands of plugins for scientific image processing and analysis into a port…	76	1029	active
3dmol/3Dmol.js 3Dmol.js is an object-oriented, WebGL-accelerated JavaScript library for interactive molecular visualization in web browsers. It supports m…	88	1028	active
jokergoo/circlize circlize is an R package for creating circular layout visualizations such as chord diagrams, circular heatmaps, and circos plots. It provid…	32	1027	stable
bxx2004/FUNGA FUNGA (Functional Gene Annotation Exploitation Platform) is an AI-powered web platform for mining gene functions, integrating cross-species…	35	1020	active
Mol* Viewer Mol* (mol-star) is a TypeScript library and technology stack for 3D visualization and analysis of large macromolecular structure data such …	93	1014	stable
BioBERT BioBERT is a pre-trained biomedical language representation model (based on BERT) with code for fine-tuning it on biomedical text mining ta…	32	2213	maintenance
lh3/bwa BWA (Burrow-Wheeler Aligner) is a command-line tool for mapping short DNA sequencing reads against large reference genomes such as the huma…	62	1768	maintenance
lucidrains/alphafold2 An unofficial PyTorch implementation of DeepMind's AlphaFold2 protein structure prediction network, built as a translation of the official …	23	1640	maintenance
kexinhuang12345/DeepPurpose DeepPurpose is a PyTorch-based deep learning library for molecular modeling, supporting drug-target interaction (DTI), drug property, drug-…	23	1197	maintenance
scipipe/scipipe SciPipe is a Go library for writing scientific workflows (pipelines) based on Flow-Based Programming, wrapping command-line tools and Go co…	23	1110	maintenance
Ligo-Biosciences/AlphaFold3 An open-source Python implementation of AlphaFold3, DeepMind's biomolecular structure prediction model, including the full model architectu…	27	1093	experimental
bcbio-nextgen bcbio-nextgen is a validated, community-developed pipeline toolkit for high-throughput sequencing analysis, including variant calling, RNA-…	23	1032	abandoned
AidLux (AidLearning) AidLux (originally AidLearning) is an AIoT development platform that runs a native Ubuntu Linux environment with GUI, deep learning tooling…	63	5812	active
DeepLabCut DeepLabCut is an open-source Python toolbox for markerless 2D and 3D pose estimation of user-defined body parts using deep neural networks …	94	5784	stable
jmiao24/Paper2Agent Paper2Agent is a multi-agent AI system that automatically converts research paper codebases into interactive AI agents with minimal human i…	61	3831	active
wolny/pytorch-3dunet A PyTorch implementation of 3D U-Net and its variants (residual, squeeze-and-excitation) for volumetric semantic segmentation, with 2D U-Ne…	57	2423	active
TileDB TileDB is an embeddable C++ storage engine for dense and sparse multi-dimensional arrays, with cloud object storage support (S3, GCS, Azure…	82	2084	stable
bowang-lab/U-Mamba U-Mamba is a hybrid CNN-state-space-model (Mamba) network for biomedical image segmentation, built on top of the nnU-Net framework. It comb…	27	1025	active
Image-Py/imagepy ImagePy is an open-source, ImageJ-like interactive image processing application and plugin framework written in Python, built on wxPython, …	23	1363	maintenance