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

Authors Yishu Wang, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri



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Yishu Wang
  • Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
  • Inria Grenoble Rhône-Alpes, Villeurbanne, France
Arnaud Mary
  • Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
  • Inria Grenoble Rhône-Alpes, Villeurbanne, France
Marie-France Sagot
  • Inria Grenoble Rhône-Alpes, Villeurbanne, France
  • Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
Blerina Sinaimeri
  • Luiss University, Rome, Italy
  • ERABLE team, Inria Grenoble Rhône-Alpes, Villeurbanne, France

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Yishu Wang, Arnaud Mary, Marie-France Sagot, and Blerina Sinaimeri. Making Sense of a Cophylogeny Output: Efficient Listing of Representative Reconciliations. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 3:1-3:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
https://doi.org/10.4230/LIPIcs.WABI.2021.3

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.

Subject Classification

ACM Subject Classification
  • Theory of computation → Dynamic programming
  • Mathematics of computing → Graph enumeration
  • Theory of computation → Backtracking
Keywords
  • Cophylogeny
  • Enumeration
  • Equivalence relation
  • Dynamic programming

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