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Figure 3

Figure 3 is comprised of a phylogenetically sorted panel of DFEs.

To recreate this figure, you must:

Perform demographic inference using Dadi

An example .bash script which performs demographic inference using Dadi for all of the species analyzed in this paper can be found at ../Scripts/fit_demographic_model.bash. Uncomment appropriate lines to do so for core genes and for accessory genes.

Fit the Distribution of Fitness Effects (DFE) using FitDadi

An example .bash script which fits the DFE using FitDadi for all of the species analyzed in this paper can be found at ../Scripts/fit_dfe.bash. Uncomment appropriate lines to do so for core genes and for accessory genes.

generate_figure_3.R

This .R script generates Figure 3 and saves it to Summary/figure_3_output.svg.