tskit_arg_visualizer: interactive plotting of ancestral recombination graphs

Journal article

Motivation: Ancestral recombination graphs (ARGs) are a complete representation of the genetic relationships between recombining lineages and are of central importance in population genetics. Recent breakthroughs in simulation and inference methods have led to a surge of interest in ARGs. However, understanding how best to take advantage of the graphical structure of ARGs remains an open question for researchers. Here, we introduce tskit_arg_visualizer, a Python package for programmatically drawing ARGs using the interactive D3.js visualization library. Results: We highlight the usefulness of this visualization tool for both teaching ARG concepts and exploring ARGs inferred from empirical datasets. Availability and implementation: The latest stable version of tskit_arg_visualizer is available through the Python Package Index (https://pypi.org/project/tskit-arg-visualizer, currently v0.1.1). Documentation and the development version of the package are found on GitHub (https://github.com/kitchensjn/tskit_arg_visualizer).

Authors: Kitchens, J; Wong, Y

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Oxford University Press
• Journal: Bioinformatics Advances
• Volume: 5
• Issue: 1
• Article number: vbaf302
• Publication date: 2025-11-24
• Acceptance date: 2025-10-12
• DOI: 10.1093/bioadv/vbaf302
• EISSN: 2635-0041
• ISSN: 2635-0041
• Language: English