.. _smcpp_demo:

=====================================
Demo: Running SMC++ on Simulated Data
=====================================

   *Running mini_smcpp on simulated genomic data.*

.. figure:: /_static/figures/fig_demo_smcpp.png
   :width: 100%
   :align: center

   **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``.
