Installation of mutpath

Requirements

You will need the following software to run mutpath.

• mutpath is written in Python. It has been tested on Mac OS X 10.6.8 with Python version 2.6.7, but it should probably work with other Python 2.6 and 2.7 versions as well.
• mutpath uses Python to do some optional graphing. To do this graphing, you need to install matplotlib. mutpath has been tested with matplotlib 1.0.0.
• Some of the scripts using MUSCLE to do sequence alignments. If you want to do these alignments, install MUSCLE. mutpath has been tested with MUSCLE version 3.8.
• You will need to install GraphViz to visualize the mutational trajectories. mutpath has been tested with GraphViz version 2.30.1 on Mac OS X 10.6.8.
• You will need BEAST and BEAGLE in appropriate versions as detailed in the next section.

Installation

To install mutpath, first download the source ZIP repository on GitHub. After unzipping the file, run the following commands:

cd mutpath
python setup.py build
python setup.py test
python setup.py install

The last command might require you to use sudo if you do not have privileges to the default installation directory. Alternatively, install it locally with:

python setup.py install --user

These commands install the Python modules and also install several scripts, which provide the most convenient high-level interface into the mutpath package. These scripts should be installed to be executable; they are present in the scripts subdirectory. The source code for the package is the in the src directory. There is also an examples subdirectory that contains some examples. Looking at these examples may be helpful for understanding the typical workflow.