pydot.InvocationException: GraphViz's executables not found
cel, answered this in the comment:
Graphviz is not a python tool. The python packages at pypi provide a convenient way of using Graphviz in python code. You still have to install the Graphviz executables, which are not pythonic, thus not shipped with these packages. You can install those e.g. with a general-purpose package manager such as homebrew
For me personally, on ubuntu 14.04, all I had to do is:
sudo apt-get install graphviz