Scripts

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:

• phyloExpCM_runcodonPhyML.py
• phyloExpCM_buildHyphyExpCM.py
• phyloExpCM_optimizeHyphyTree.py
• phyloExpCM_ExpModelOptimizeHyphyTree.py
• phyloExpCM_FreqsFromAlignment.py
• phyloExpCM_SiteLikelihoodComparison.py
• phyloExpCM_multiHyphyRuns.py