This repository contains the code to compute the distance to the stochastic phylogenetic varieties, for the case presented in the paper Computing the distance to the positive part of phylogenetic varieties by M. Casanellas, J. Fernández-Sánchez and M. Garrote López submitted as a Computation Presentation at the MEGA 2019 conference.
Macaulay2 and PHCpack should be previously installed.
File AlgorithmStochasticPhylogeneticVarieties.m2 contains the main code.
The following lines are comented in the code since the execution of them could take several days. Uncomment them in case you want to compute the degree for different parameters.
J = saturate(ideal I, ideal(x_0*x_1*x_2*x_3*x_4));
degJ = degree J;
Substitute parameters k0 and m0 for desired values
k0 = 2/10;
m0 = 14/10;