/slime

A package for simulating tree sequences with local ancestry information.

Primary LanguagePythonMIT LicenseMIT

slime

slime is a package for simulating admixed tree sequences with local ancestry information.

slime combines two existing tree sequence simulation softwares, SLiM and msprime. Admixed history is simulated forward-in-time with SLiM, while ancient history of the admixing populations is simulated backwards-in-time with msprime.

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/

Documentation

https://slime.readthedocs.io/en/latest/