tracts#
A Python library for demographic inference from ancestry tracts.
Main guidelines to use tracts.
End-to-end examples with figures and code.
A tutorial to compute Phase-Type distributions from a migration matrix.
Detailed reference for modules, functions, and classes.
tracts models migration histories in admixed populations using ancestry tracts.
It supports multiple source populations, time-dependent migration, sex-biased admixture and inference for both autosomes and the X chromosome.
Installation#
git clone https://github.com/gravelLab/tracts.git
cd tracts
pip install .
You can now import tracts as a python package.
Note
tracts is currently not distributed on PyPI or Conda.
The papers#
A detailed introduction to the models and methods presented in tracts 2.0 is available in this paper (in preparation). tracts 1.0 is based on this paper.
Updates in tracts 2.0
Software updates
tractsis now a Python package rather than a single.pyfile.tractsno longer requires writing a custom driver script.Demographic models are now defined via YAML.
Methodological updates
Phase-Type theory for tract distributions.
X chromosome support.
Sex-biased migration.
Improved admixture models.
Contact#
For any inquires, please file an issue or contact us.