The evolutionary, demographic, and phylogeographic histories of viral pathogens can be inferred from their genomic sequence data. Bayesian phylogeographic approaches, for example, can be used to reconstruct the spatial dynamics of pathogen transmission. Although a range of tools is available for evolutionary analyses of viral pathogens, these typically focus on specific stages of the workflow, leaving a need for an integrated framework. We introduce VirPhyKit, a toolkit that integrates 12 specialized modules through an intuitive point-and-click interface. VirPhyKit streamlines key tasks in phylogeographic analysis, including sequence curation, spatiotemporal subsampling, migration pattern analysis, and molecular dating. Furthermore, it offers built-in functionality to generate high-quality figures that are suitable for publication. As a stand-alone application supported on Windows and Linux operating systems, VirPhyKit promises to be a valuable resource for researchers studying viral ecology and evolution. The software and source code are available at https://github.com/BioEasy/VirPhyKit.
Keywords: Bayesian phylogeography; data subsampling; molecular dating; region‐randomization test; spatial diffusion.
© 2025 The Author(s). Ecology and Evolution published by British Ecological Society and John Wiley & Sons Ltd.