Ricci-Ollivier curvature of SPR and related graphs.
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analysis
figs
gricci @ 67f8efe
prefigs
random_spr_walk @ 0026fbd
scripts
spr_neighbors @ d9def7d
svg_figs
tables
tangle @ 1647506
.gitignore
.gitmodules
IEEEtran.bst
IEEEtran.cls
README.md
SConstruct
curvature.bib
curvature.tex
elsarticle-num.bst
elsarticle.cls
ltexpprt.sty
ltexpprt.tex
response_to_reviewers.txt
response_to_reviewers_2.txt
spr-curvature.ipynb

README.md

curvature

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.

Software dependencies

In addition to Sage, we depend on the following python packages:

  • scons
  • matplotlib
  • seaborn
  • pandas

Running analyses

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.

Handy commands

git pull --recurse-submodules
git submodule update --recursive