Demographic Inference in Polyploids

Read the Docs

This repository hosts all the code for testing models for demographic inference in polyploid species. The models are implemented in the open-source Python package dadi.

Each folder corresponds to a different analysis from the accompanying manuscript (link). More detailed documentation can be found on our Read the Docs website (link above), as well as within the comments of the scripts in this repository.

Note

While working on the manuscript we changed the homoeologous exchange parameter from $d_{i \leftrightarrow j}$ to $e_{i \leftrightarrow j}$. Because, of this some of the code may still have dij as a parameter but it represents the same thing.

Preprint information

Blischak, PD, M Sajan, MS Barker, RN Gutenkunst. 2022. Demographic history inference and the polyploid continuum. bioRxiv doi: https://doi.org/10.1101/2022.09.15.508148.