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Making Sense of a Cophylogeny Output: Efficient Listing of Representative Reconciliations

Abstract : Cophylogeny reconciliation is a powerful method for analyzing host-parasite (or host-symbiont) co-evolution. It models co-evolution as an optimization problem where the set of all optimal solutions may represent different biological scenarios which thus need to be analyzed separately. Despite the significant research done in the area, few approaches have addressed the problem of helping the biologist deal with the often huge space of optimal solutions. In this paper, we propose a new approach to tackle this problem. We introduce three different criteria under which two solutions may be considered biologically equivalent, and then we propose polynomial-delay algorithms that enumerate only one representative per equivalence class (without listing all the solutions). Our results are of both theoretical and practical importance. Indeed, as shown by the experiments, we are able to significantly reduce the space of optimal solutions while still maintaining important biological information about the whole space.
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https://hal.inria.fr/hal-03295799
Contributor : Marie-France Sagot <>
Submitted on : Thursday, July 22, 2021 - 12:23:21 PM
Last modification on : Thursday, September 16, 2021 - 10:25:45 AM

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Yishu Wang, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri. Making Sense of a Cophylogeny Output: Efficient Listing of Representative Reconciliations. WABI 2021 - 21st International Workshop on Algorithms in Bioinformatics, Aug 2021, Chicago, United States. pp.1-18, ⟨10.4230/LIPIcs.WABI.2021.3⟩. ⟨hal-03295799⟩

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