This is the text and code for the paper Ricci-Ollivier curvature of the rooted phylogenetic Subtree-Prune-Regraft graph by Chris Whidden and Erick Matsen.
In addition to Sage, we depend on the following python packages:
SConstruct file in
analysis according to needs, and then type
scons on the command line in the
analysis directory to run the analyses.
Additional plotting and regression is performed in the IPython notebook
git pull --recurse-submodules git submodule update --recursive