Case-of-mpox-due-to-monkeypox-virus-clade-Ia-infection-detected-in-Ireland

This repository contains data and scripts related to the publication "Case of mpox due to monkeypox virus clade Ia infection detected in Ireland".

Source data for Figure 3 (Panels A and B)

Includes the phylogenetic tree file used for tree visualisation of panel A (957_seq.treefile) and panel B (subcluster.tree), the mutation annotation file used to generate the stacked mutation rectangles in Panel B (mutations.txt), and the output from squirrel (https://github.com/aineniamh/squirrel) used to derive the mutation counts (subcluster.tree.branch_snps.reconstruction.csv). Also includes the R script used to generate the figure (Figure1_phylogenetic_trees.R).