Simulating population pangenomes under coalescent demographic models with MSpangenome

Motivation: Pangenome variation graphs (PVGs) are increasingly used to represent genomic diversity, yet there is currently no general framework for generating population pangenomes directly from explicit evolutionary histories. Existing simulators typically focus on individual classes of variation and do not integrate these variations within a genealogy-aware framework driven by explicit demographic histories. As a result, evaluating pangenome methods in realistic population-genetic settings remains challenging, and benchmark datasets with known evolutionary ground truth are scarce. Results: We present MSpangenome, a genealogy-aware frame- work that bridges coalescent population genetic simu