Raw data and scripts for bioinformatic analyses conducted for:
Gomez JB., Barrick JE, Waters CM (2025) Phages use contingency loci as a bet-hedging strategy. bioRxiv. https://doi.org/10.1101/2025.10.21.683753
Instructions: Navigate into each folder and execute the bash and R scripts in the order 01, 02, 03, etc. to produce processed data files and plots.
Install/Dependencies: This workflow was tested on MaxOSX 15.7.1. The bash script and python scripts it invokes were run using a conda environment with python 3.11.8, biopython 1.81, and pandas 2.0.3 installed. R scripts were executed in RStudio 2025.09.2+418 with R 4.4.2 and tidyverse 2.0.0, ggplot2 4.0.1, patchwork 1.3.2, stringi 1.8.7, and multcompView 0.1-10 libraries installed.