MMseqs2: ultra fast and sensitive search and clustering suite

An Attention-based Ensemble Learning Framework for Protein Design

Public Release of ProGen3 family of Models

DSPy: The framework for programming—not prompting—language models

LLM agents built for control. Designed for real-world use. Deployed in minutes.

Official release of the ProGen models

Hierarchical Reasoning Model Official Release

Guarded Resampling for Safe and Automated Machine Learning in R

PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **technical issues** on this repository (e.g., compiling, programs a…

ColabFold on your local PC

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

Scripts to add mmseqs MSA/templates to alphafold3 input json and also custom template files

🧬 Augmenting zero-shot mutant prediction by retrieval-based logits fusion. (ISMB/ECCB 2025)

🏭 Easy data acquisition, benchmark resources, PLM fine-tuning for bio-researchers. (ACL Demo 2025)

Updated Protpardelle models with more robust motif scaffolding and multichain support

A Privacy-Preserving Framework Based on TensorFlow

This package contains deep learning models and related scripts for RoseTTAFold

hybrid assembly pipeline for bacterial genomes

A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.

Data repository for "Fine-tuning protein language models boosts predictions across diverse tasks"

Updated version of CRISPRDetect.

List of software/websites/databases/other stuff for genome engineering

Predicting high-fitness mutations based on protein inverse folding models