License: Creative Commons Attribution 4.0 International license (CC BY 4.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.WABI.2021.3
URN: urn:nbn:de:0030-drops-143564
URL: https://drops.dagstuhl.de/opus/volltexte/2021/14356/
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Wang, Yishu ; Mary, Arnaud ; Sagot, Marie-France ; Sinaimeri, Blerina

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

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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.

BibTeX - Entry

@InProceedings{wang_et_al:LIPIcs.WABI.2021.3,
  author =	{Wang, Yishu and Mary, Arnaud and Sagot, Marie-France and Sinaimeri, Blerina},
  title =	{{Making Sense of a Cophylogeny Output: Efficient Listing of Representative Reconciliations}},
  booktitle =	{21st International Workshop on Algorithms in Bioinformatics (WABI 2021)},
  pages =	{3:1--3:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-200-6},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{201},
  editor =	{Carbone, Alessandra and El-Kebir, Mohammed},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/opus/volltexte/2021/14356},
  URN =		{urn:nbn:de:0030-drops-143564},
  doi =		{10.4230/LIPIcs.WABI.2021.3},
  annote =	{Keywords: Cophylogeny, Enumeration, Equivalence relation, Dynamic programming}
}

Keywords: Cophylogeny, Enumeration, Equivalence relation, Dynamic programming
Collection: 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)
Issue Date: 2021
Date of publication: 22.07.2021


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