# pysinger

A pure-Python rewrite of the [SINGER](https://github.com/popgenmethods/SINGER) Bayesian ARG sampler.

```{admonition} Disclaimer
:class: important

This project was set up mainly as an **educational resource for myself** to understand the SINGER algorithm by reimplementing it from scratch. All intellectual credit belongs to the original authors. **For production use, the authoritative reference, and the optimised C++ implementation, please refer to the original repository:**

**[github.com/popgenmethods/SINGER](https://github.com/popgenmethods/SINGER)**
```

> Deng, Y., Nielsen, R. & Song, Y.S. Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes. *Nature Genetics* **57**, 2124--2135 (2025). [doi:10.1038/s41588-025-02317-9](https://doi.org/10.1038/s41588-025-02317-9)

```{toctree}
:maxdepth: 2

overview
build_singer_yourself
theory
data_structures
hmm
mcmc
io
api
```