Lorax

Lorax is a web-native platform for real-time, interactive visualization and exploration of population-scale Ancestral Recombination Graphs.

• CLI entrypoint: lorax (alias: lorax-arg)

Key features

• Scalable rendering: interactive visualization of ARGs at a biobank scale.
• 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 (pip)

conda create -n lorax-runtime python=3.11 pip -c conda-forge
conda activate lorax-runtime
python -m pip install lorax-arg
lorax # this opens lorax in a browser

lorax --file # to directly load file on lorax (preferred for large files.)

Use a dedicated environment instead of Conda base so NumPy, Numba, tskit, and PyArrow are resolved as one compatible stack.

Preprocessed CSR artifacts adjacent to a tree-sequence file are enabled by default in the pip app. To disable them, launch with LORAX_CSR_ARTIFACTS_ENABLED=0 lorax.

Input Formats Tree sequences: .trees and .trees.tsz files (compatible with tskit/tsinfer/tsdate, Relate, ARGweaver output) CSV: One row per recombination interval with columns for genomic position, Newick tree string, tree depth, and optional metadata. Ideal for custom inference pipelines or non-model organisms.

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

Links

Web platform: https://lorax.ucsc.edu Source code: https://github.com/pratikkatte/lorax