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 havedijas 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.