Metadata-Version: 2.4
Name: lorax-arg
Version: 0.1.8
Summary: Interactive ARG visualization for genomics
Author: Lorax Team
License-Expression: MIT
Project-URL: Homepage, https://lorax.in
Project-URL: Documentation, https://lorax.in
Project-URL: Source, https://github.com/pratikkatte/lorax
Project-URL: Issues, https://github.com/pratikkatte/lorax/issues
Keywords: lorax,arg,ancestral recombination graph,tree sequence,visualization,genomics,evolution,phylogenetics,bioinformatics
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Environment :: Console
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License-File: LICENSE
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Dynamic: license-file

# 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`)

![Lorax demo](https://raw.githubusercontent.com/pratikkatte/lorax/main/docs/images/lorax-demo-2.gif)
## 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)

```bash
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
