Skip to content


Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?

Latest commit


Git stats


Failed to load latest commit information.
Latest commit message
Commit time

Build Status Docs

BVAS: Bayesian Viral Allele Selection

Welcome to the GitHub repository for Inferring selection effects in SARS-CoV-2 with Bayesian Viral Allele Selection. The results from our main analysis are available in paper. More recent inference results are also available: 08.10.22, 09.22.22, 05.18.23, 06.15.23, 06.30.23, 07.11.23, 09.13.23, and 09.20.23. Thanks to Benjamin Kotzen (@bkotzen) for help generating these more recent results!


BVAS requires Python 3.8 or later and the following Python packages: PyTorch, pandas, and pyro.

Note that if you wish to run BVAS on a GPU you need to install PyTorch with CUDA support. In particular if you run the following command from your terminal it should report True:

python -c 'import torch; print(torch.cuda.is_available())'

Installation instructions

Install directly from GitHub:

pip install git+

Install from source:

git clone
cd bvas 
pip install .


The documentation is available here.

Repo organization

This repo is organized as follows:

  • bvas: all the core code: inference algorithms and simulations
  • paper: some of the figures and inference results contained in the paper
  • notebooks: Jupyter notebooks demonstrating BVAS usage
  • data: pre-processing scripts and (some of the) data used in the analysis
  • docs: source code for the documentation
  • example_scripts: example scripts that demo BVAS usage
  • tests: unit tests for verifying the correctness of inference algorithms and other code