This repo contains simulation and analysis code for the manuscript:

Jiang, C. J., & Weissman, D. B. (2026). Bursts of reproduction can create genetic structure in frequently recombining bacterial populations. GENETICS. https://doi.org/10.1093/genetics/iyag132

Project organization

Simulation parameters and seeds are stored as .json files.

Scripts to generate figures in figures_manuscript/

• Fig 1: example_tree.py
• Fig 2: kingman_progression.py
  • Runs in runs/*
• Fig 3: r_d_distribution_arity.py
  • Runs simulated with cluster/mass_sim_arity.py
• Fig 4: structure_platter.py
  • Runs in runs_structured/*
• Fig 5: three_peaks_segments.py
  • Values in subplots D, E, and F computed using pair_segments.py
• Fig 6: liu_and_good.py
  • Runs in runs/* and runs_structured/151.json
  • Fraction of identical blocks computed using cluster/frac_iden_blk.py

Additionally, many scripts were reused across many figures for common tasks:

• Simulations run using cluster/sim.py.
  
• Pairwise distances computed using cluster/dist.py
• $$\bar r_d$$ computed using cluster/rd.py
• Fraction of a pair's genome clonally inherited using cluster/frac_clonal.py

Some extra scripts for exploratory/miscellaneous plotting in ./plt_* and figures_others/