Welcome to slime’s documentation!

Introduction

This is the documentation for slime, the local ancestry simulator.

Note

This documentation is incomplete and under development.

Under the hood, each slime simulation consists of 3 components:

1. A forward-in-time simulation of admixture using SLiM.
2. A backwards-in-time simulation of ancestral population history using msprime.
3. Extraction of local ancestry from the resulting tree sequence.

Installation

Ensure you have pip installed and type this into your command line:

pip install -i https://test.pypi.org/simple/ slime

You will also need to install SLiM. Instructions are here:

https://messerlab.org/slim/