New software for visualising ARGs and tree sequences

New software for visualising ARGs and tree sequences

The standard visualization of a tree sequence is as a set of adjacent trees. However, the set of correlated trees in a tree sequence can also be thought of as a single graph structure. A new D3-based project called tskit_arg_visualiser by James Kitchens (left), a graduate student in the Coop lab in UC Davis, allows you to visualize these graphs, interactively manipulate node positions, and more. This is a great way to produce graphics for demos, posters, teaching etc.

The visualizer can be embedded in notebooks or web pages, and can draw “orthogonal” style classic Ancestral Recombination Graphs, or diagonal-line-style graphs that are more suitable for simplified ARGs such as standard msprime output.

This is an early release, and more features are planned. Check out the interactive examples in the tskit visualization tutorial and the tskit ARG tutorial, or head over to the GitHub repo for installation instructions or to help out with development.