Impossibility results on stability of phylogenetic consensus methods

Requirements

• Python 2.7
• Gurobi >= 7.5 (free academic licences are available)
• Gurobipy

Usage

For n=5 leaves, both programs need around 8 Gigabytes of RAM.

Extension stability on binary trees

python extension.py [-h] [-t THREADS] [n]

Find a regular consensus method that satisfies extension stability on profiles of two binary trees.

Positional arguments:

  n                     number of leaves (between 3 and 5, default 3)

Optional arguments:

  -h, --help            show help message and exit
  -t THREADS, --threads THREADS
                        number of threads that can be used

Associative stability

python associative.py [-h] [-t THREADS] [n]

Find a regular consensus method that is associative and Pareto on rooted triples.

Positional arguments:

  n                     number of leaves (between 3 and 5, default 3)

Optional arguments:

  -h, --help            show help message and exit
  -t THREADS, --threads THREADS
                        number of threads that can be used