Clustering the Space of Maximum Parsimony Reconciliations in the Duplication-Transfer-Loss Model.

Phylogenetic tree reconciliation is widely used in the fields of molecular evolution, cophylogenetics, parasitology, and biogeography for studying the evolutionary histories of pairs of entities. Reconciliation is often performed using maximum parsimony under the DTL (Duplication-Transfer-Loss) event model. Since the number of maximum parsimony reconciliations (MPRs) can be exponential in the sizes of the trees, an important problem is that of finding a small number of representative reconciliations. We give a polynomial time algorithm that can be used to find the cluster representatives of the space of MPRs with respect to a number of different clustering algorithms and specified number of clusters.