Comparing amino-acid preferences across influenza HA subtypes

Study by Jenny Ahn, Timothy Yu, and Jesse Bloom. See Ahn and Yu et al (2026) for details on the study.

Conda environment

Build the conda environment using the provided environment.yml file in this directory:

conda env create -f environment.yml 

Snakemake pipeline

Some of the analyses are automated by snakemake. To run the pipeline:

conda activate ha-epistasis
snakemake -j 8 -s Snakefile --rerun-incomplete

To run on the Hutch cluster via slurm, you can run:

sbatch -c 8 run_hutch_cluster.bash

Note some parts of the analysis depend on a local installation of ChimeraX. The files in data/rmsd were pre-generated so that the pipeline runs in a single go, but they depend on files generated in the pipeline. If you'd like to reproduce them, open the ChimeraX scripts rmsd_ha1.cxc and rmsd_ha2.cxc in ChimeraX.

This pipeline builds HTML documentation in ./docs/. These docs are rendered for viewing at https://jbloomlab.github.io/ha-preference-shifts/.