Mutations in half or more of sequences for pango-designated SARS-CoV-2 lineages

Sets of designated pango lineages

A tool to determine protein sequences for SARS-CoV-2 lineages

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

Code for designing biased protein states

Tools for evolutionary forecasting

Code for the paper "OneProt: Towards Multi-Modal Protein Foundation Models"

Accurate Species Tree EstimatoR: a family of optimation algorithms for species tree inference (including ASTRAL & CASTER)

Accurate Species TRee ALgorithm

Guide Tree Merger

A comprehensive collection of KAN(Kolmogorov-Arnold Network)-related resources, including libraries, projects, tutorials, papers, and more, for researchers and developers in the Kolmogorov-Arnold N…

Long read production pipelines

Statistical inference of growth-based deep mutational scanning (DMS) screens

A Snakemake-based pipeline for analyzing DMS data, as used with Rosace

Observed substitution counts of SARS-CoV-2 compared to those expected under the mutation rates

SARS-CoV-2 RBD antibody escape calculator

Official code repository for the paper "ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers"

Official repository for the ProteinGym benchmarks

Deep mutational scanning of the SARS-CoV-2 3CL protease

Graph Positional and Structural Encoder

Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.