In this paper, we present an integer linear programming (ILP) approach, called  CoRe-ILP , for finding an optimal time consistent cophylogenetic host-parasite reconciliation under the cophylogenetic event model with the events cospeciation, duplication, sorting, host switch, and failure to diverge. Instead of assuming event costs, a simplified model is used, maximizing primarily for cospeciations and secondarily minimizing host switching events. Duplications, sortings, and failure to diverge events are not explicitly scored. Different from existing event based reconciliation methods,  CoRe-ILP  can use (approximate) phylogenetic branch lengths for filtering possible ancestral host-parasite interactions. Experimentally, it is shown that  CoRe-ILP   can successfully use branch length information and performs well for biological and simulated data sets. The results of  CoRe-ILP  are compared with the results of the reconciliation tools   Jane 4 ,  Treemap 3b ,  NOTUNG 2.8 Beta , and   Ranger-DTL . Algorithm  CoRe-ILP  is implemented using  IBM ILOG CPLEX  Optimizer 12.6 and is freely available from http://pacosy.informatik.uni-leipzig.de/core-ilp.
['Nicolas Wieseke', 'Tom Hartmann', 'Matthias Bernt', 'Martin Middendorf']
Cophylogenetic Reconciliation with ILP