CoRe-ILP is a tool for reconciling the phylogenetic trees of parasites with the trees of their respective hosts. It uses a simple event model, considering cospeciations and host switching events. Based on this model solutions with a maximal number of cospeciations (primary criterion), a minimal number of host switching events (secondary criterion), and a minimal number of interactions (tertiary criterion) is found. CoRe-ILP is feasible for cophylogenetic systems with multi-host parasites and polytomies and uses branch length information, provided with the trees, to filter possible solutions.
Implemented as Integer Linear Program, CoRe-ILP is feasible for computing optimal solutions of cophylogenetic systems with up to 100 species.
CoRe-ILP relies on the IBM ILOG CPLEX Optimizer 12.6. for which an academic license can be obtained for free.Download CoRe-ILP from here.