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On the Ancestral Compatibility of Two Phylogenetic Trees with Nested Taxa

Journal of Mathematical Biology volume 53, pages 340–364 (2006)Cite this article

Abstract

Compatibility of phylogenetic trees is the most important concept underlying widely-used methods for assessing the agreement of different phylogenetic trees with overlapping taxa and combining them into common supertrees to reveal the tree of life. The notion of ancestral compatibility of phylogenetic trees with nested taxa was recently introduced. In this paper we analyze in detail the meaning of this compatibility from the points of view of the local structure of the trees, of the existence of embeddings into a common supertree, and of the joint properties of their cluster representations. Our analysis leads to a very simple polynomial-time algorithm for testing this compatibility, which we have implemented and is freely available for download from the BioPerl collection of Perl modules for computational biology.

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Affiliations

  1. Department of Mathematics and Computer Science, Research Institute of Health Science, University of the Balearic Islands, 07122, Palma de Mallorca, Spain

    Mercè Llabrés, Jairo Rocha & Francesc Rosselló

  2. Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, 08034, Barcelona, Spain

    Gabriel Valiente

Authors
  1. Mercè Llabrés
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  2. Jairo Rocha
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  3. Francesc Rosselló
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  4. Gabriel Valiente
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Correspondence to Gabriel Valiente.

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Llabrés, M., Rocha, J., Rosselló, F. et al. On the Ancestral Compatibility of Two Phylogenetic Trees with Nested Taxa. J. Math. Biol. 53, 340–364 (2006). https://doi.org/10.1007/s00285-006-0011-4

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  • DOI: https://doi.org/10.1007/s00285-006-0011-4

Keywords

  • Phylogenetic tree
  • Compatibility
  • Topological embedding

Mathematics Subject Classification (2000)

  • 05C05
  • 92D15
  • 92B10