Data and scripts from: Revealing reassortment in influenza A viruses with TreeSort
This repository contains scripts and data to replicate the experiments from
Markin, 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/10.1101/2024.11.15.623781
For 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.
Funding
USDA-ARS: 5030-32000-231-000D
USDA-ARS: 5030-32000-231-080-I
USDA-ARS: 0500-00093-001-00-D
NIAID CENTERS OF EXCELLENCE FOR INFLUENZA RESEARCH AND RESPONSE (CEIRR)
National Institute of Allergy and Infectious Diseases
Find out more...Centers for Disease Control and Prevention: 21FED2100395IPD
Center for Disease Control and Prevention: 24FED2400250IPC
History
Data contact name
Markin, AlexeyData contact email
alexey.markin@usda.govPublisher
Ag Data CommonsTemporal Extent Start Date
2024-11-01Theme
- Non-geospatial
ISO Topic Category
- health
National Agricultural Library Thesaurus terms
Influenza A virus; birds; swine; humans; genomics; disease transmission; pandemic; phylogeny; genes; hosts; avian influenza; surface proteins; viruses; risk assessmentOMB Bureau Code
- 005:18 - Agricultural Research Service
OMB Program Code
- 005:040 - National Research
ARS National Program Number
- 103
Pending citation
- No
Public Access Level
- Public
