Demo: Running SMC++ on Simulated Data

Running mini_smcpp on simulated genomic data.

SMC++ demo on msprime-simulated data. Panel A: Input heterozygosity tracks from multiple diploid genomes simulated under a bottleneck history. Panel B: SMC++ emission probabilities for het/hom observations at different coalescence times – P(het|k) rises with coalescence time as mutation accumulates. Panel C: ODE solution for undistinguished lineage probabilities P(J(t)=j) across time intervals under the bottleneck demography. Panel D: Effective coalescence rate h(t) under bottleneck, constant, and expansion demographic histories.

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