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
K-Dense-AI/scientific-agent-skills Scientific Agent Skills is a Python library that provides a collection of validated procedural skills and access to over 100 scientific dat…	80	52679	active
cytoscape/cytoscape.js Cytoscape.js is a fully featured graph theory (network) library written in pure JavaScript for modelling, analysing, and visualising relati…	97	11236	stable
google-deepmind/alphafold3 Google DeepMind's official implementation of the AlphaFold 3 inference pipeline for predicting biomolecular structures and interactions. It…	81	8643	active
DeepChem DeepChem is a Python library that democratizes deep learning for drug discovery, quantum chemistry, materials science, and biology. It prov…	63	7050	active
Biopython Biopython is a widely used open-source Python library of tools for computational molecular biology and bioinformatics. It provides modules …	76	5223	stable
attractivechaos/klib Klib is a standalone, lightweight C library of generic data structures and algorithms implemented largely as single-header files using C ma…	55	4730	stable
jwohlwend/boltz Boltz is a family of open-source biomolecular interaction models (Boltz-1 and Boltz-2) that predict complex structures and binding affiniti…	58	4257	active
ArcInstitute/evo2 Evo 2 is a DNA foundation language model (1B-40B parameters) that models genomes at single-nucleotide resolution with up to 1 million base …	56	4247	active
snap-stanford/Biomni Biomni is a general-purpose biomedical AI agent from Stanford that autonomously executes research tasks across biomedical subfields. It com…	68	3923	active
google/deepvariant DeepVariant is a deep learning-based genomic variant caller that converts aligned DNA sequencing reads (BAM/CRAM) into pileup image tensors…	78	3818	stable
RDKit RDKit is an open-source cheminformatics toolkit written in C++ with Python, Java, C#, and JavaScript wrappers. It provides core data struct…	95	3597	stable
google-deepmind/alphafold Open-source implementation of the AlphaFold 2 inference pipeline for predicting protein structures from amino acid sequences, including Alp…	54	14887	maintenance
Nextflow Nextflow is an open-source DSL and runtime for building scalable, portable, and reproducible data-driven computational pipelines, based on …	100	3514	stable
aqlaboratory/openfold OpenFold is a faithful, trainable PyTorch reproduction of DeepMind's AlphaFold 2 for protein structure prediction. It is memory-efficient a…	45	3435	active
google-deepmind/science-skills A collection of agent skills from Google DeepMind that extend AI coding agents with structured instructions, scripts, and references for sc…	81	3263	active
OpenWorm OpenWorm is an open-source project building a comprehensive bottom-up computational model of the Caenorhabditis elegans roundworm, integrat…	75	3063	active
RFDiffusion RFdiffusion is an open-source method for de novo protein structure generation using diffusion models, with or without conditional informati…	59	3058	active
Biohub/esm A Python library and model release providing ESMC protein language models, ESMFold2 structure prediction, and the ESM Atlas of 6.8 billion …	88	2987	active
sokrypton/ColabFold ColabFold is a set of tools and Google Colab notebooks that make protein structure prediction with AlphaFold2, AlphaFold3, ESMFold, and rel…	92	2940	active
Snakemake Snakemake is a Python-based workflow management system for creating reproducible and scalable data analyses. Workflows are defined via a re…	93	2880	stable
satijalab/seurat Seurat is an R toolkit for single-cell genomics developed by the Satija Lab, providing a complete pipeline for analyzing single-cell RNA-se…	88	2803	stable
scverse/scanpy Scanpy is a scalable Python toolkit for analyzing single-cell gene expression data, built alongside the anndata data structure. It provides…	92	2574	stable
OpenGene/fastp fastp is an ultra-fast all-in-one FASTQ preprocessing and quality control tool written in C++. It handles adapter trimming, quality filteri…	98	2435	stable
MouseLand/cellpose Cellpose is a generalist deep learning algorithm for cellular and nucleus segmentation in microscopy images, with human-in-the-loop capabil…	80	2371	active
neuropsychology/NeuroKit NeuroKit2 is a Python library for neurophysiological and biosignal processing, offering easy access to advanced routines for signals like E…	76	2366	active
RosettaCommons/RoseTTAFold RoseTTAFold is the official implementation of a deep learning system for predicting protein structures and interactions using a three-track…	23	2269	stable
alexdobin/STAR STAR (Spliced Transcripts Alignment to a Reference) is a fast, splice-aware aligner for RNA-seq reads written in C++. It aligns reads to a …	24	2262	active
lh3/minimap2 minimap2 is a fast, versatile pairwise sequence aligner for genomic and spliced (RNA-seq) nucleotide sequences, written in C. It maps long …	70	2260	stable
AlphaGenome A Python SDK providing programmatic access to Google DeepMind's AlphaGenome model, which predicts genomic regulatory outputs such as gene e…	89	2192	active
soedinglab/MMseqs2 MMseqs2 is an open-source C++ suite for ultra-fast, sensitive search and clustering of huge protein and nucleotide sequence sets, running o…	69	2147	active
bytedance/Protenix Protenix is an open-source PyTorch reproduction of AlphaFold 3 for high-accuracy biomolecular structure prediction, covering proteins, nucl…	78	2070	active
broadinstitute/gatk GATK (Genome Analysis Toolkit) is the Broad Institute's industry-standard toolkit for analyzing high-throughput DNA and RNA sequencing data…	84	2003	active
chaidiscovery/chai-lab Chai-1 is a state-of-the-art multi-modal foundation model for biomolecular structure prediction, handling proteins, small molecules, DNA, R…	62	2001	active
OpenMM OpenMM is a high-performance toolkit and library for molecular dynamics simulation, with optimized GPU-accelerated kernels. It can be used …	94	2000	stable
allenai/scispacy scispaCy is a Python library providing full spaCy pipelines, models, and custom pipes for processing scientific, biomedical, and clinical t…	47	1994	active
aipoch/medical-research-skills A curated library of 550+ SKILL.md-compatible agent skills for medical and biomedical research, covering evidence insights, protocol design…	70	1971	active
samtools/samtools SAMtools is a suite of C command-line programs, built on HTSlib, for reading, writing, editing, indexing, sorting, and viewing SAM/BAM/CRAM…	93	1963	stable
dauparas/ProteinMPNN ProteinMPNN is a PyTorch-based tool that designs amino acid sequences for given protein backbone structures using a message-passing neural …	23	1872	stable
Galaxy Galaxy is an open-source, web-based platform for accessible, reproducible, and transparent data-intensive scientific research, primarily in…	92	1869	stable
rust-bio/rust-bio Rust-Bio is a Rust library providing implementations of algorithms and data structures useful for bioinformatics, such as sequence alignmen…	88	1840	stable
schrodinger/pymol-open-source The open-source foundation of PyMOL, a molecular visualization system for rendering and analyzing 3D structures of proteins, nucleic acids,…	71	1748	active
lucidrains/alphafold3-pytorch A PyTorch implementation of Google DeepMind's Alphafold 3 model for protein and molecular structure prediction. It is a research-oriented r…	67	1699	active
scvi-tools scvi-tools is a Python library for deep probabilistic modeling and analysis of single-cell and spatial omics data, built on PyTorch, PyTorc…	92	1697	stable
MDAnalysis/mdanalysis MDAnalysis is an open-source Python library for analyzing molecular dynamics simulations of many-body systems at the molecular scale. It re…	69	1650	stable
bowang-lab/scGPT scGPT is a foundation model for single-cell multi-omics built with a generative transformer, providing pretrained checkpoints and a Python …	64	1646	active
shenwei356/seqkit SeqKit is an ultrafast, cross-platform command-line toolkit written in Go for manipulating FASTA and FASTQ sequence files, offering 38+ sub…	88	1596	active
DeepGraphLearning/torchdrug TorchDrug is a PyTorch-based machine learning library for drug discovery, covering graph neural networks, deep generative models, and reinf…	23	1589	active
gcorso/DiffDock DiffDock is a deep learning implementation of a diffusion generative model for molecular docking, predicting how small molecule ligands bin…	28	1585	active
evo-design/evo Evo is a 7-billion-parameter DNA foundation model built on the StripedHyena architecture, trained on ~300 billion tokens of prokaryotic who…	65	1576	active
lh3/seqtk Seqtk is a fast, lightweight C command-line toolkit for processing sequences in FASTA and FASTQ formats, with optional gzip support and onl…	30	1564	stable
google/neuroglancer Neuroglancer is a WebGL-based, client-side web application for visualizing large 3-D volumetric datasets, supporting arbitrary cross-sectio…	77	1562	active
ComplexHeatmap An R/Bioconductor package for creating complex heatmaps with flexible arrangement of multiple heatmaps and rich annotation graphics. It is …	53	1559	active
ANTs Advanced Normalization Tools (ANTs) is a C++ command-line library for high-dimensional medical image registration and segmentation, built o…	81	1505	active
MultiQC/MultiQC MultiQC is a Python command-line tool that scans directories for log files and outputs from 150+ bioinformatics tools and aggregates them i…	85	1492	stable
qupath/qupath QuPath is an open-source desktop application for bioimage analysis, aimed especially at digital pathology and whole-slide imaging. It provi…	75	1450	active
imagej/imagej2 ImageJ2 is an open-source Java framework and application for processing and analyzing N-dimensional scientific image data, built on the Img…	72	1411	stable
openbabel/openbabel Open Babel is an open-source chemical toolbox that reads, writes, converts, searches, and analyzes chemical data across more than 100 molec…	88	1384	stable
K-Dense-AI/k-dense-byok K-Dense BYOK is a free, open-source desktop application providing 'Kady', an AI research assistant (co-scientist) that runs locally and use…	78	1376	active
Quilt Data Platform Quilt is a scientific data management platform built on AWS that turns S3 data into deeply versioned, metadata-rich data packages for teams…	67	1373	active
nf-core/rnaseq nf-core/rnaseq is a Nextflow-based bioinformatics pipeline for analyzing RNA sequencing data, performing QC, trimming, (pseudo-)alignment w…	85	1371	active
SRA Toolkit The NCBI SRA Toolkit is a collection of command-line tools and libraries for accessing, converting, and downloading data from the INSDC Seq…	75	1368	active
nextstrain/ncov A Nextstrain build pipeline that analyzes SARS-CoV-2 viral genomes to understand their evolution and spread, producing phylogenetic visuali…	82	1363	active
vgteam/vg vg is a C++ toolkit for building, manipulating, and analyzing genome variation graphs (pangenome graphs). It provides succinct graph data s…	92	1343	active
bbuchfink/diamond DIAMOND is a BLAST-compatible local sequence aligner for protein and translated DNA searches, designed for high-performance analysis of lar…	97	1326	active
agemagician/ProtTrans ProtTrans provides state-of-the-art pre-trained Transformer language models for protein sequences, trained on thousands of GPUs and hundred…	29	1326	active
steineggerlab/foldseek Foldseek is a command-line tool for fast and sensitive comparison, search, and clustering of large protein 3D structure sets, including mon…	65	1299	active
microsoft/BioGPT BioGPT is Microsoft's domain-specific generative Transformer language model pre-trained on biomedical text, with implementation code and pr…	10	4491	maintenance
stardist/stardist StarDist is a Python library for object detection and instance segmentation in 2D and 3D microscopy images using star-convex shapes, built …	54	1271	stable
scikit-bio scikit-bio is an open-source, BSD-licensed Python library providing data structures, algorithms, and educational resources for bioinformati…	89	1246	active
YuLab-SMU/clusterProfiler An R/Bioconductor package for functional enrichment analysis (ORA, GSEA, topology-aware) of omics data across thousands of species. It prov…	76	1239	active
martinpacesa/BindCraft BindCraft is a Python-based computational pipeline for de novo protein binder design that combines AlphaFold2 backpropagation, ProteinMPNN,…	68	1216	active
omicverse/omicverse OmicVerse is a Python library for multi-omics analysis covering bulk, single-cell, and spatial RNA-seq workflows. It is part of the scverse…	93	1209	active
scverse/gget gget is a free, open-source Python package and command-line tool for efficiently querying genomic reference databases such as Ensembl, UniP…	93	1204	active
a-r-j/graphein Graphein is a Python library for constructing graph and mesh representations of proteins, RNA, molecules, and biological interaction networ…	74	1197	active
facebookresearch/esm Meta FAIR's Evolutionary Scale Modeling (ESM) library providing Transformer protein language models with pretrained weights, including ESM-…	10	4170	maintenance
shenwei356/csvtk csvtk is a cross-platform command-line toolkit written in Go for manipulating CSV/TSV tabular data. It provides many subcommands for filter…	93	1171	active
deepmodeling/Uni-Mol Uni-Mol is a collection of 3D molecular representation learning frameworks and pretrained models for tasks like molecule property predictio…	30	1167	active
ClawBio/ClawBio ClawBio is a bioinformatics-native AI agent skill library offering 97 curated, reproducible skills for genomics tasks like pharmacogenomics…	81	1155	active
ScorpioLea/AiCE AiCE is a Python tool that predicts high-fitness protein mutations by sampling sequences from protein inverse folding models such as Protei…	37	1144	active
paulvangentcom/heartrate_analysis_python HeartPy is a Python library for analyzing heart rate from PPG (photoplethysmography) and ECG signals, including noisy and low-resolution we…	46	1143	active
CellProfiler CellProfiler is a free, open-source desktop application for quantitative analysis of biological images, letting biologists build modular im…	67	1137	active
shenwei356/rush rush is a cross-platform command-line tool written in Go for executing jobs in parallel, similar to GNU parallel. It supports custom variab…	88	1134	active
WojciechMula/pyahocorasick A Python module (implemented as a C extension with a pure-Python fallback) implementing the Aho-Corasick algorithm for fast multi-pattern s…	69	1126	stable
moshi4/pyCirclize pyCirclize is a Python package built on matplotlib for creating circular visualizations such as Circos plots, chord diagrams, and radar cha…	66	1122	active
PaddlePaddle/PaddleHelix PaddleHelix is a bio-computing platform built on PaddlePaddle featuring large-scale representation learning and multi-task deep learning fo…	53	1120	active
OpenSim OpenSim Core is a C++ library and set of command-line applications for building musculoskeletal models and running dynamic simulations of m…	82	1119	stable
PharMolix/OpenBioMed OpenBioMed is an open-source toolkit and agent platform for biomedicine and life science, offering multimodal models like BioMedGPT-Mol, 45…	69	1104	active
SimpleITK/SimpleITK SimpleITK is a simplified C++ interface to the Insight Toolkit (ITK) for multi-dimensional image analysis, including filtering, segmentatio…	96	1092	stable
kblin/ncbi-genome-download A Python command-line tool for downloading bacterial, fungal, viral, and other genome files from NCBI's FTP servers in GenBank, FASTA, and …	53	1089	active
broadinstitute/cromwell Cromwell is an open-source Workflow Management System from the Broad Institute that executes scientific workflows written in WDL (Workflow …	76	1083	active
CJ-Chen/TBtools-II TBtools-II is a stand-alone bioinformatics platform with a user-friendly GUI and command-line tools for analyzing high-throughput sequencin…	86	1082	active
HannesStark/boltzgen BoltzGen is an open-source all-atom generative diffusion model for designing protein and peptide binders against arbitrary biomolecular tar…	75	1081	active
ccsb-scripps/AutoDock-Vina AutoDock Vina is an open-source molecular docking engine used for predicting how small molecules bind to protein targets. It supports fast …	70	1081	active
hail-is/hail Hail is an open-source Python library for scalable exploration and analysis of genomic data, built on Spark, Scala, and C++ primitives for …	88	1080	active
broadinstitute/picard Picard is a set of Java command line tools from the Broad Institute for manipulating high-throughput sequencing data in formats such as SAM…	79	1080	stable
bigdatagenomics/adam ADAM is a genomics analysis platform built on Apache Spark that provides schemas and APIs for processing genomic data like reads, variants,…	52	1061	active
bedtools bedtools is a suite of command-line utilities for genome arithmetic, enabling set-theory operations like intersect, merge, count, complemen…	58	1054	stable
wu-yc/LabClaw LabClaw is a modular library of 240 SKILL.md agent skills for biomedical AI research, covering biology, drug discovery, medicine, data scie…	45	1053	active
cBioPortal cBioPortal is an open-source web application for visualization, analysis, and download of large-scale cancer genomics datasets. This reposi…	92	1048	active
xuzhougeng/wisp-science Wisp Science is an open-source, local-first desktop AI research workbench that combines an LLM agent with persistent Python/R kernels, MCP-…	77	1047	active