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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

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tskit_arg_visualizer: interactive plotting of ancestral recombination graphs.

James Kitchens¹, Yan Wong²

¹Department of Evolution & Ecology and Center for Population Biology, University of California-Davis, Davis, CA 95616, United States.

Bioinformatics Advances

|December 15, 2025

Summary

This study introduces tskit_arg_visualizer, a Python package for visualizing ancestral recombination graphs (ARGs). The tool aids in teaching ARG concepts and exploring complex genetic data from population genetics research.

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Area of Science:

Population Genetics
Computational Biology
Bioinformatics

Background:

Ancestral recombination graphs (ARGs) are crucial for understanding genetic relationships in recombining lineages.
Recent advancements in ARG simulation and inference have increased their importance in population genetics.
Effective utilization of ARG graphical structures remains an active research area.

Purpose of the Study:

To introduce tskit_arg_visualizer, a novel Python package for programmatic visualization of ARGs.
To provide researchers with a tool to better understand and explore ARG structures.
To facilitate both educational purposes and the analysis of empirically inferred ARGs.

Main Methods:

Development of a Python package, tskit_arg_visualizer.
Integration with the D3.js library for interactive visualizations.
Programmatic generation of ARG plots.

Main Results:

tskit_arg_visualizer enables the creation of visualizations for ARGs.
The tool is effective for teaching fundamental ARG concepts.
It supports the exploration of ARGs derived from real-world genetic datasets.

Conclusions:

tskit_arg_visualizer offers a valuable resource for population geneticists.
The package enhances the accessibility and interpretability of complex genetic relationship data.
It bridges the gap between ARG theory and practical data analysis.