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AI-assisted mutation nomination approach optimizing protein function by integrating structural and evolutionary constraints into protein inverse folding models, compatible with ProteinMPNN, LigandMPNN, ESM-IF1, and SaProt (Chinese Academy of Sciences, 359+ stars)

Another list focuses on Python stuff related to Chemistry.

Cheminformatic extension for the SQLAlchemy database.

SIMD C library for global, semi-global, and local pairwise sequence alignments

NIST's open-source platform for data-driven atomistic materials design, integrating DFT datasets (JARVIS-DFT), machine learning property prediction (JARVIS-ML), and a comprehensive leaderboard for benchmarking materials AI methods across the periodic table (384+ stars)

Large-scale flow-based protein backbone generator utilizing hierarchical fold class labels for conditioning with a tailored scalable transformer architecture, enabling controllable de novo protein design (264+ stars)

DeepSeek's open-source large language model for formal theorem proving in Lean 4, integrating informal and formal mathematical reasoning through recursive subgoal decomposition and reinforcement learning powered by DeepSeek-V3, with open weights and ProverBench evaluation (2025)

In silico directed evolution framework using few-shot active learning to optimize protein activities, enabling rapid protein engineering with minimal experimental data (352+ stars, 2023)

GRIDSS: the Genomic Rearrangement IDentification Software Suite.

Systematic medical RAG toolkit for question answering over PubMed, StatPearls, textbooks, and Wikipedia, supporting multiple retrievers, domain LLMs, and follow-up-query workflows for benchmarked clinical/biomedical QA (ACL Findings 2024)

General-purpose pathology foundation model pretrained on 100K+ diagnostic whole-slide images across 20 major tissue types, achieving state-of-the-art transfer learning across 30+ clinical tasks and serving as a universal feature extractor for digital pathology (Mahmood Lab, 722+ stars)

Vision-language pathology foundation model using contrastive learning on histopathology image-text pairs, enabling zero-shot classification, slide-level retrieval, and multimodal reasoning across diverse cancer types (Mahmood Lab, 494+ stars)

Python wrapper for [bedtools](https://github.com/arq5x/bedtools).

Democratizing AlphaFold3: PyTorch reimplementation to accelerate protein structure prediction research

Descriptor computation(chemistry) and (optional) storage for machine learning.

SKESA is a de-novo sequence read assembler for microbial genomes. It uses conservative heuristics and is designed to create breaks at repeat regions in the genome. This leads to excellent sequence quality without significantly compromising contiguity.

Universal chart comprehension and reasoning model

Circlator is a tool to circularize genome assemblies. It will attempt to identify each circular sequence and output a linearised version of it. It does this by assembling all reads that map to contig ends and comparing the resulting contigs with the input assembly.

k-mer counting, filtering, and graph traversal.

NOVOPlasty - The organelle assembler and heteroplasmy caller. NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes..

A VCF Parser for Python.

Displaying sequence statistics for next-generation sequencing.

Educational resource on performing RNA-seq analysis in the cloud using Amazon AWS cloud services. Topics include preparing the data, preprocessing, differential expression, isoform discovery, data visualization, and interpretation.

Open source web framework for small molecule analysis based on Django.

Learning nonlinear operators

AI for chemical reaction prediction and synthesis planning

FASTQ/A short-reads pre-processing tools: Demultiplexing, trimming, clipping, quality filtering, and masking utilities.

Finds SNP sites from a multi-FASTA alignment file.

Customizable pipeline for differential expression analysis with an intuitive GUI.

Flexible circular visualization of genome-associated data with BioPerl and SVG.

Horizon chart D3-based JavaScript library for DNA data.