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EUCALYPT: efficient tree reconciliation enumerator.

Beatrice Donati1,2,3, Christian Baudet1,2, Blerina Sinaimeri1,2

  • 1Inria Grenoble - Rhône-Alpes; Inovallée 655, avenue de l'Europe, Montbonnot, Saint Ismier cedex, 38334 France.

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Summary
This summary is machine-generated.

Phylogenetic tree reconciliation helps understand host-parasite coevolution. A new algorithm, Eucalypt, efficiently enumerates all optimal reconciliations, addressing limitations of previous methods and aiding biological interpretation.

Keywords:
CophylogenyEnumeration algorithmHost-parasite systemsPolynomial delayReconciliation

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Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Phylogenetic tree reconciliation analyzes organism coevolution using event-based maximum parsimony.
  • Enumerating all optimal reconciliations is crucial for biological interpretation but current algorithms have limitations.
  • Existing methods fail to produce all possible solutions or handle all cost vectors.

Purpose of the Study:

  • To develop a comprehensive algorithm for enumerating all optimal phylogenetic reconciliations.
  • To assess the interpretability challenges posed by the large number of potential optimal solutions.
  • To introduce a restricted reconciliation model to manage solution complexity.

Main Methods:

  • Developed a polynomial-delay algorithm for enumerating all optimal reconciliations.
  • Analyzed the number and classification of solutions under various cost models.
  • Introduced and analyzed a restricted reconciliation model with distance constraints on host switches.

Main Results:

  • The new algorithm enumerates all optimal reconciliations with polynomial delay.
  • A high number of optimal solutions (e.g., 5120 for small trees) can exist, even for time-feasible reconciliations.
  • Classifying solutions by event counts can reduce complexity, but numbers can remain substantial.
  • A restricted model reduces solution counts while preserving optimal cost or finding near-optimal solutions.

Conclusions:

  • Eucalypt is a novel, freely available algorithm for enumerating all optimal reconciliations.
  • The study highlights the significant number of optimal solutions and proposes methods for managing their interpretation.
  • A restricted reconciliation approach offers a practical way to handle complex coevolutionary scenarios.