Data and scripts from: Revealing reassortment in influenza A viruses with TreeSort

<p dir="ltr">This repository contains scripts and data to replicate the experiments from<br>Markin, A., Macken, C.A., Baker, A.L., and Anderson, T.K., 2024. <b>Revealing reassortment in influenza A viruses with TreeSort</b>. bioRxiv 2024.11.15.623781; doi: <a href="https://doi.org/10.1101/2024.11.15.623781" rel="noreferrer" target="_blank">https://doi.org/10.1101/2024.11.15.623781</a></p><p><br></p><p><br></p><p dir="ltr">For the TreeSort tool and tutorial, see <a href="https://github.com/flu-crew/TreeSort" rel="noreferrer" target="_blank">https://github.com/flu-crew/TreeSort</a>.</p><p dir="ltr">Unzip TreeSort-experiments.zip and see the nested directories and README files for instructions to replicate the study.</p><p dir="ltr">- See 'simulations' directory for code and instructions to replicate the simulation study.<br>- See 'IAV-reasortment-analysis' directory for data and code to replicate the analysis of reassortment rates and patterns among avian, swine, and human IAV lineages.</p><p dir="ltr"><br></p><p dir="ltr">Contact alexey.markn@usda.gov for questions.</p><p dir="ltr"><br></p>