Pop lab
=======

Population genetics simulations for the classroom.

Simulation applications
=======================

One locus forward in time
-------------------------

These applications simulate the classic one locus with two alleles scenario in one or more populations.
They can be used to explore: drift, selection, mutation, migration and selfing.
For more details use the applications or read their :doc:`documentation <practices/fwd/one_locus>`.

.. grid:: 2

   .. grid-item-card:: Drift
      :link: simple_drift

   .. grid-item-card:: Selection
      :link: simple_selection

   .. grid-item-card:: Balancing selection
      :link: balancing_selection

   .. grid-item-card:: One locus general
      :link: one_locus

Coalescence
-----------

The following set of applications simulate the evolution of a genomic region, with mutation, drift, recombination and selection, in different demographic scenarios using a coalescence approach.
For more details read the :doc:`coalescence simulation documentation <practices/coalescence/coalescence>`

.. grid:: 2

   .. grid-item-card:: Bottleneck
      :link: bottleneck

   .. grid-item-card:: Founder effect
      :link: founder

   .. grid-item-card:: Drifting pops.
      :link: drifting_pops

   .. grid-item-card:: Admixture
      :link: admixture


Population genetic practices
============================

One locus
---------

.. grid:: 2

   .. grid-item-card:: Drift
      :link: practices/fwd/drift.html

      Allele frequency drift

   .. grid-item-card:: Selection
      :link: practices/fwd/selection.html

      Positive and negative selection

   .. grid-item-card:: Balancing selection
      :link: practices/fwd/balancing_selection.html

      Balancing selection with differing selection preasures in different populations


One genomic region
------------------

.. grid:: 2

   .. grid-item-card:: Bottleneck
      :link: practices/coalescence/bottleneck.html

      Bottleneck impact on diversity

   .. grid-item-card:: Founder effect
      :link: practices/coalescence/founder.html

      Drift due to the founder effect

   .. grid-item-card:: Drifting pops.
      :link: practices/coalescence/drifting_pops.html

      Three pops. drifting from one ancestral pop.

   .. grid-item-card:: Admixture
      :link: practices/coalescence/admixture.html

      Population creating by merging two populations.



.. toctree::
   :maxdepth: 1
   :hidden:

   practices/fwd/drift
   practices/fwd/selection
   practices/fwd/balancing_selection
   practices/fwd/one_locus
   practices/coalescence/bottleneck
   practices/coalescence/founder
   practices/coalescence/drifting_pops
   practices/coalescence/admixture