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:
sconsmatplotlibseabornpandas
Edit the 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 analysis/plot-and-regress.ipynb.
git pull --recurse-submodules
git submodule update --recursive