Data and scripts from: Revealing reassortment in influenza A viruses with TreeSort
This repository contains scripts and data to replicate the experiments fromMarkin, A., Macken, C.A., Baker, A.L., and Anderson, T.K., 2024. Revealing reassortment in influenza A viruses with TreeSort. bioRxiv 2024.11.15.623781; doi: https://doi.org/10.1101/2024.11.15.623781For the TreeSort tool and tutorial, see https://github.com/flu-crew/TreeSort.Unzip TreeSort-experiments.zip and see the nested directories and README files for instructions to replicate the study.- See 'simulations' directory for code and instructions to replicate the simulation study.- 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.Contact alexey.markn@usda.gov for questions.
Find Related Datasets
Search by Tags
Click any tag below to search for similar datasets
Complete Metadata
| @type | dcat:Dataset |
|---|---|
| accessLevel | public |
| bureauCode |
[ "005:18" ] |
| contactPoint |
{ "fn": "Markin, Alexey", "hasEmail": "mailto:alexey.markin@usda.gov" } |
| description | <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> |
| distribution |
[ { "@type": "dcat:Distribution", "title": "TreeSort-experiments.zip", "format": "zip", "mediaType": "application/zip", "downloadURL": "https://ndownloader.figshare.com/files/51224678" } ] |
| identifier | 10.15482/USDA.ADC/28039040.v1 |
| keyword |
[ "Influenza A", "Reassortment" ] |
| license | https://creativecommons.org/publicdomain/zero/1.0/ |
| modified | 2025-05-06 |
| programCode |
[ "005:040" ] |
| publisher |
{ "name": "Agricultural Research Service", "@type": "org:Organization" } |
| temporal | 2024-11-01/2024-11-01 |
| title | Data and scripts from: Revealing reassortment in influenza A viruses with TreeSort |
