Year: 2024
Type: article
Abstract: 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).
Source: Bioinformatics Advances
Authors: James Kitchens, Yan Wong
Institutions: University of California, Davis, University of Oxford
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,917
OpenAlex ID: W4416582181