Supplementary files for "Generation of Tree-Child phylogenetic networks"

By G. Cardona and J.C. Pons

If you have pipenv installed, the requirements can be installed by executing pipenv install. Notice however that graphviz must be installed previously (only needed to run the Jupyter notebook). Once installed, the jupyter notebooks can be run with pipenv run jupyter-notebook, and the scripts with pipenv run python script.py.

The jupyter notebook can also be run without installing anything:

The included files are:

• generating_TC.py: Python module that generates BTC networks.
• bounds.py: Python script that computes the upper bound for the number of BTC networks. It runs without parameters and computes these bounds up to 10 leaves.
• compute_offspring.py: Python script that computes the offspring of a set of networks. Usage: compute_offspring.py infile outfile taxon. infile is a text file containing the eNewick strings of the networks whose offspring has to be computed; outfile text file where the eNewick strings of the offspring are written; taxon identifier for the new taxon to be used for the generated networks.
• count_offspring.py: Python script that computes the cardinality of the offspring of a set of networks. Usage: count_offspring.py infile. infile is a text file containing the eNewick strings of the networks whose offspring has to be counted.
• nets_n.txt: Text file containing the eNewick strings of the BTC networks with n leaves (for n=1,2,3,4). These files can be used as input for the scripts above.
• demo.ipynb: Jupyter notebook that demonstrates the sequential and random generation of BTC networks with arbitrary number of leaves, as well as some computations using the module generating_TC.py.