NB: Simulating new data sets and analyzing any of the data files requires a few pieces of software. To simulate new data sets using the code provided in the tutorial, you will need ms and Seq-Gen. To analyze the data sets and any of the results files you will need to install HyDe.

The file HyDe.ipynb is a Jupyter Notebook with a walkthrough of the analyses that we conducted as part of our talks at Evolution.

• data.txt and map.txt: these are simulated data sets that ca be during these the tutorial to test out the different features of HyDe. The code to generate them is in the HyDe.ipynb notebook.

• heliconius-out.txt and heliconius-boot.txt: these are the results files from our analysis of the Heliconius data set from Martin et al. (2013).

• swordtail-out.txt: this is the result file from our analysis of the swordtail data set from Cui et al (2013).