This repo is organized into different sections:

• snakemake: All large-scale, computationally-intense data processing was done with Snakemake. More information about individual processing tasks can be seen in this folder.
• analysis: All exploratory analyses, plotting, and statistical testing.
• scripts: Scripts used throughout the data processing or analyses portions of this project.
• supp_tables: Miscellaneous code related to cleaning the tables used for the final Supplementary tables.
• ref: Assorted files either used as or directly derived from reference annotations / genomes.