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Scripts
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Installation of `mapmuts`_ installs a set of scripts that can be run directly from the command line. These scripts perform all of the main functions of the package. You should be able to utilize the full functionality simply by running these scripts, without interacting directly with the Python code.

.. toctree::
   :maxdepth: 1

   mapmuts_makealignments
   mapmuts_alignmentsummaryplot
   mapmuts_parsecounts
   mapmuts_parsesummaryplots
   mapmuts_countparsedmuts
   mapmuts_inferpreferences
   mapmuts_inferdifferentialpreferences
   mapmuts_preferencescorrelate
   mapmuts_preferencemeans
   mapmuts_siteprofileplots
   mapmuts_entropycomparison

Other scripts
----------------
Here are some other scripts that are part of the package. These scripts are not part of the recommended workflow as they have been replaced by other scripts or seem to be unnecessary. However, they are still distributed with the package and might be of use for some application.

.. toctree::
   :maxdepth: 1

   mapmuts_aafracsplots
   mapmuts_inferenrichment
   mapmuts_enrichmentcorrelate
   mapmuts_enrichmentgeomeans

.. include:: weblinks.txt