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Flex-sweep documentation
========================

Second version of `Flex-sweep <https://doi.org/10.1093/molbev/msad139>`_, a versatile tool for detecting selective sweeps. The software simulates, estimates summary statistics, and trains a convolutional neural network (CNN) to classify genomic regions as sweeps or neutrals.


.. toctree::
   :maxdepth: 2
   :caption: Contents:

   introduction
   installation
   basic_usage
   scan
   prediction
   enrichment
   polarize
   advanced_usage
   api


Citing Flex-sweep
-----------------

If you use flexsweep in your research, please cite:

Lauterbur, M.E., Munch, K. and Enard, D. (2023) Versatile detection of diverse selective sweeps with flex-sweep, *Molecular Biology and Evolution*, 40(6).

Kern, A.D. and Schrider, D.R. (2016). discoal: flexible coalescent simulations with selection. *Bioinformatics*, 32(24), 3839-3841.

Support
-------

 * Report issues on `GitHub <https://github.com/jmurga/flexsweep>`_

 * Contact: murgamoreno@arizona.edu, denard@arizona.edu

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.. API