This is the GitHub repository for Mah, Lohmueller, and Garud 2023, BioRxiv. The entirety of the project and the work that went into it is available via the commit history; however, for ease of viewing, we have organized the directory with helpful .md documents describing how to recreate the figures and tables in our study.

This directory includes the following subdirectories:

• Analysis: Analysis of Data, as well as several .md documents describing how to reproduce each figure and table in the main text and supplement.
• Data: Data and Results.
• Scripts: Scripts used for analysis and plotting.
• Summary: Figures and Tables for inclusion in the main text, as well as intermediate output
• Supplement: All supplemental tables and figures
• microbiome_evolution_master: Inherited code from Garud and Good et al. 2019, PLoS Biology

Consult download_data.md.

Consult 'MIDAS.md'.

An example .bash script which constructs synonymous and nonsynonymous SFSs for all of the species analyzed in this paper can be found at ./Scripts/compute_sfs.bash. Uncomment appropriate lines to do so for core genes and for accessory genes.

An example .bash script which downsamples SFSs to 14 alleles, as was done for all of the species analyzed in this paper, can be found at ./Scripts/downsample_sfs.bash.