Epidemiological inference for emerging viruses using segregating sites

This repository contains code and data for the manuscript titled "Epidemiological inference for emerging viruses using segregating sites".

Epidemiological inference for emerging viruses using segregating sites Yeongseon Park, Michael Martin, Katia Koelle bioRxiv 2021.07.07.451508; doi: https://doi.org/10.1101/2021.07.07.451508

Example command line to run analysis:

python piuss.py \
    --inputData  "../simualted_data/SEIR_prop500_full.tsv" \
    --config     "config/config_simulated_full_2Dgridsearch"