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Scripts
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Installation of `phyloExpCM`_ 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.

Here are the scripts:

.. toctree::
   :maxdepth: 1

   phyloExpCM_runcodonPhyML
   phyloExpCM_buildHyphyExpCM
   phyloExpCM_optimizeHyphyTree
   phyloExpCM_ExpModelOptimizeHyphyTree
   phyloExpCM_FreqsFromAlignment
   phyloExpCM_SiteLikelihoodComparison
   phyloExpCM_multiHyphyRuns



.. include:: weblinks.txt