pipeline to study lineage rate variation's effect on f4 stats

Code to reproduce the simulation study in: Frankel & Ané (2025) "Low accuracy of complex admixture graph inference from f-statistics".

Preprint available here: https://www.biorxiv.org/content/10.1101/2025.03.07.642126v1

goal and model

Goal: simulate sequence data (SNPs) under a network model reflecting archaic human population genetics with ILS and lineage rate variation, to answer these questions:

1. How does f4 perform when there is lineage rate variation?
2. How much lineage rate variation causes consequential type-1 error, or a reduction in power?
3. How are the admixture graphs inferred from f4 results affected?

dependencies

• julia packages: see Project.toml
• seqgen for the simulation of sequences: Seq-Gen v1.3.4 downloaded from github at commit from 2019-08-29.
• R packages:
  • SiPhyNetwork version 1.1.0, see notes/software_install.md
  • admixtools, see notes/software_install.md