Demo: Running PSMC on Simulated Data

Running mini_psmc on simulated genomic data.

PSMC demo on msprime-simulated data. Panel A: Input heterozygosity sequence from a diploid genome simulated under a bottleneck demographic model. Panel B: True N(t) piecewise demographic history with PSMC time discretization intervals shown as vertical lines. Panel C: Posterior decoding heatmap of HMM hidden states (coalescence time intervals) along the genome, using the true parameters. Panel D: True coalescence time vs MAP hidden state, illustrating how the HMM assigns genomic positions to time intervals.

This figure was generated by running the mini_psmc implementation on data simulated with msprime. The script is at figures/fig_demo_psmc.py.