First install git, then clone our repository with

git clone https://github.com/cpmoni/igl-polyhedra.git

This package requires some dependencies:

• cycler version 0.10.0
• decorator version 4.1.2
• DendroPy version 4.3.0
• functools32 version 3.2.3.post2
• matplotlib version 2.0.2
• networkx version 1.11
• numpy version 1.13.1
• pyparsing version 2.2.0
• python-dateutil version 2.6.1
• pytz version 2017.2
• six version 1.10.0
• subprocess32 version 3.2.7

To automatically install the package dependencies listed above, install pip and run:

pip install requirements.txt

python connection_graph.py <input_filename> <output_filename>

This script generates the BHV connection graph for moving between multiple copies of BHV space-those with maximal dimensional orthants of which the dimension is determined by the number of leaves of an unrooted tree, and described in the manuscript available at https://arxiv.org/abs/1708.02626

To move from one copy of BHV space to another we have adopted the convention of starting in a lower dimension and moving to higher dimensions. Therefore a start tree is necessary to use our code.

The input file should contain the start tree in Newick format in the first line, and the list of new leaves in the second line in parenthesis, for example: (10, 11, 12). Please use numbers as the labels of the leaves in the start tree and the new leaves. The default input file is "start_tree.tre".

The program will display the connection graph and save it to <output_filename>. It also prints out the number of nodes and edges in the graph.

If you have any questions feel free to contact us at redavid2@illinois.edu.