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: Several
.mddocuments describing how to reproduce each figure and table in the main text and supplement. - Data: Intermediate files used by Scripts
- HighRecombinationAnalysis: Model and empirical site-frequency-spectra derived from HighRecombinationData
- HighRecombinationData: Intermediate files used by Scripts to produce the files in HighRecombinationAnalysis.
- Scripts: Scripts used for analysis and plotting.
- Summary: Figures and Tables for inclusion in the main text, as well as some intermediate outputs
- Supplement: All supplemental tables and figures
- SupplementaryAnalysis: Over the course of revisions, we substantially augmented our data set. This directory contains model and empirical site-frequency-spectra used for the revised version of our manuscript.
- 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. To construct SFS's while removing regions of low recombination and selective sweeps, instead you may consult ./Scripts/high_recombination.bash.
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.