BindCraft modified to make PyRosetta use and installation optional: no license needed

A collection of resources on attention-based graph neural networks

DeepSpeed is a deep learning optimization library that makes distributed training and inference easy, efficient, and effective.

An open-source deep learning framework for data mining of protein-protein interfaces or single-residue variants.

MMseqs2: ultra fast and sensitive search and clustering suite

AlphaFold 3 inference pipeline.

CLOCI (Co-occurrence Locus and Orthologous Cluster Identifier) identifies gene clusters using multiple proxies of selection for coordinated gene evolution. In the process, CLOCI circumscribes loci …

Scripts to download genomes from the NCBI FTP servers

Searching for precursor peptide genes for ribosomally synthesized and post-translationally modified peptides (RiPPs).

Practical Cheminformatics Tutorials

The official codebase of the paper "Chemical language modeling with structured state space sequence models"

codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, prophage, etc.) relative to the full genome.

Reaction Analysis through Imaging of Chemical Units

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtool…

Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes

(Meta-)genome screening for functional and natural product gene sequences

Earl Grey: A fully automated TE curation and annotation pipeline

Create a phylogenetic tree with an absence/presence matrix of biosynthetic gene clusters

Create a phylogenetic tree with an absence/presence matrix of biosynthetic gene clusters

genEra is a fast and easy-to-use command-line tool that estimates the age of the last common ancestor of protein-coding gene families.

STRIDE: Species Tree Root Inference from Gene Duplication Events

Transformer model for gene symbol assignment of protein coding sequences

Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)

Color AlphaFold predicted models by pLDDT scores

Recurrent Geometric Networks for end-to-end differentiable learning of protein structure

Container for PKS Predictor TransAtor