We have developed software called Phylotree as a toolkit for running experiments to study gene cophylogenies for genome evolution using distance-based methods. In particular, the toolkit has been instrumental in conducting processing-heavy experiments with the new “difference of means” statistical method. Phylotree was used to run experiments using simulated data as well as biological sequences of well known host and parasite species, and is distributed with data and configuration files allowing these experiments to be reproduced
