.. _clues_demo:

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Demo: Running CLUES on Simulated Data
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   *Running mini_clues on simulated genomic data.*

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

   **CLUES demo of selection inference.** Panel A: Wright-Fisher allele frequency trajectories under different selection coefficients. Panel B: Transition matrix difference between selection and neutrality, showing how selection biases frequency changes. Panel C: Likelihood surface over selection coefficient values. Panel D: Beta-quantile frequency bin discretization with finer resolution at the boundaries.

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