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.

CoRe-ILP Downloads

Download CoRe-ILP
Download Source code

Results of all Simulation experiments from the Publication (including the scripts for reevaluation)

CoRe-ILP is executed from the command line using:

java -jar CoRe-ILP.jar -i <input file> -o <output file>

use --help for an overview on CoRe-ILP‘s parameters

Note that IBM ILOG CPLEX Optimizer 12.6 is required for running CoRe-ILP. Depending on your os and architecture, just copy the respective library, libcplex126.jinilib or cplex126.dll to CoRe-ILP‘s subfolder os/[linux|macosx|windows]/[x86|x86_64]. The respective file is contained in the IBM ILOG CPLEX Optimizer 12.6 distribution. Java 1.6 or later has to be installed on your system.

To run CoRe-ILP with the other versions of IBM ILOG CPLEX Optimizer use one of the following links.
CPLEX 12.7.1: CoRe-ILP1271
CPLEX 12.9.0: CoRe-ILP1290
CPLEX 12.10.0: CoRe-ILP12100

Feel free to send bug reports or any other kind of impressions or suggestions on CoRe-ILP to

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CoRe-ILP Publications

Reference for CoRe-ILP:

N. Wieseke, T. Hartmann, M. Bernt, and M. Middendorf
Cophylogenetic Reconciliation with ILP
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12(6): 1227-1235, 2015.
Preliminary version presented at Asia Pacific Bioinformatics Colloquium (APBC 2015), Taiwan, 2015 (accepted September 2014)
Workprint and Supplement

The conference program can be downloaded from here.