dikeledik/Influenza-A-H1N1-pdm09-in-South-Africa-2018-2024-Manuscript-

Scripts, input and XML files used for the analysis of the South African A(H1N1)pdm09 viruses for Manuscript # Data and code for The evolution of influenza A(H1N1)pdm09 in South Africa—2018-2024 ## Overview This repository contains the analysis files, supporting input data and visualisation scripts associated with the manuscript: **“The evolution of influenza A(H1N1)pdm09 in South Africa—2018-2024.” Virus Evolution, 2026.** The repository is intended to support transparency and reproducibility by providing the files needed to inspect the analysis configuration and reproduce the figures presented in the manuscript. ## Repository contents ### BEAST XML files Each directory contains the XML configuration files used for the BEAST analyses described in the manuscript. To protect sensitive or restricted data, the original nucleotide or amino-acid sequence characters have been removed from the publicly available XML files. Sequence characters have been replaced with missing-data symbols while preserving the XML structure, taxon identifiers, alignment lengths, model settings, priors, operators, and MCMC configuration. Consequently, the redacted XML files document the analytical configuration but cannot reproduce the complete analyses without access to the original sequence data. ### Input data Each directory contains input data used for downstream analyses and visualisation. These files include posterior estimates generated by the analyses. ### Visualisation scripts Each directory contains the scripts used to process the analysis outputs and generate the figures included in the manuscript. The scripts were written in R.