Representing a Set of Reconciliations in a Compact Way

Comparative genomic studies are often conducted by reconciliation analyses comparing gene and species trees. One of the issues with reconciliation approaches is that an exponential number of optimal scenarios is possible. The resulting complexity is masked by the fact that a majority of reconciliation software pick up a random optimal solution that is returned to the end-user. However, the alternative solutions should not be ignored since they tell different stories that parsimony considers as viable as the output solution. In this paper, we describe a polynomial space and time algorithm to build a minimum reconciliation graph--a graph that summarizes the set of all most parsimonious reconciliations. Amongst numerous applications, it is shown how this graph allows counting the number of non-equivalent most parsimonious reconciliations.