Lorax

Interactive visualization and exploration of Ancestral Recombination Graphs (ARGs)

Web platform: lorax.ucsc.edu | Pip package: lorax-arg

Key Features

• Scalable rendering -- Interactive visualization of ARGs at biobank scale using WebGL
• Genome-wide navigation -- Traverse genomic coordinates and inspect local genealogies at recombination breakpoints
• Mutation-aware -- Trace variant inheritance through local genealogies
• Metadata integration -- Filter, color, and subset samples by population labels, phenotypes, or custom annotations
• Flexible inputs -- Supports .trees, .trees.tsz (tskit tree sequences), and CSV-based ARG representations

Quick Start

Install with pip (recommended)

pip install lorax-arg
lorax

This opens Lorax in your browser. To load a file directly (preferred for large files):

lorax --file path/to/your.trees

Run with Docker

docker pull pratikkatte7/lorax
docker run -it -p 80:80 lorax

Then open http://localhost:80 in your browser.

For more installation options (building from source, Docker builds, volume mounting, environment variables), see INSTALL.md.

Supported Input Formats

Format	Description
.trees, .trees.tsz	compatible with tskit tree sequences files; .trees.tsz is a tszip-compressed variant.
.csv	One row per recombination interval with genomic position, Newick tree, depth, and optional metadata

Use Cases

• Explore signatures of natural selection in local genealogies
• Visualize introgression and admixture across genomic regions
• Trace ancestry of specific samples through population-scale ARGs
• Navigate from GWAS hits or functional annotations to underlying genealogical structure

Citation

If you use Lorax in your research, please cite:

Lorax: Interactive visualization of Ancestral Recombination Graphs. https://github.com/pratikkatte/lorax

License

Lorax is released under the MIT License.

Maintainer

Pratik Katte
Department of Biomolecular Engineering & Bioinformatics
University of California, Santa Cruz