| Summary: | Abstract Background Maximum parsimony reconciliation in the duplication-transfer-loss model is a widely-used method for analyzing the evolutionary histories of pairs of entities such as hosts and parasites, symbiont species, and species and genes. While efficient algorithms are known for finding maximum parsimony reconciliations, the number of such reconciliations can be exponential in the size of the trees. Since these reconciliations can differ substantially from one another, making inferences from any one reconciliation may lead to conclusions that are not supported, or may even be contradicted, by other maximum parsimony reconciliations. Therefore, there is a need to find small sets of best representative reconciliations when the space of solutions is large and diverse. Results We provide a general framework for hierarchical clustering the space of maximum parsimony reconciliations. We demonstrate this framework for two specific linkage criteria, one that seeks to maximize the average support of the events found in the reconciliations in each cluster and the other that seeks to minimize the distance between reconciliations in each cluster. We analyze the asymptotic worst-case running times and provide experimental results that demonstrate the viability and utility of this approach. Conclusions The hierarchical clustering algorithm method proposed here provides a new approach to find a set of representative reconciliations in the potentially vast and diverse space of maximum parsimony reconciliations.
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