Journal of Mathematical Biology

, Volume 53, Issue 3, pp 340–364 | Cite as

On the Ancestral Compatibility of Two Phylogenetic Trees with Nested Taxa

  • Mercè Llabrés
  • Jairo Rocha
  • Francesc Rosselló
  • Gabriel Valiente


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.


Phylogenetic tree Compatibility Topological embedding 

Mathematics Subject Classification (2000)

05C05 92D15 92B10 


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Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Mercè Llabrés
    • 1
  • Jairo Rocha
    • 1
  • Francesc Rosselló
    • 1
  • Gabriel Valiente
    • 2
  1. 1.Department of Mathematics and Computer Science, Research Institute of Health ScienceUniversity of the Balearic IslandsPalma de MallorcaSpain
  2. 2.Algorithms, Bioinformatics, Complexity and Formal Methods Research GroupTechnical University of CataloniaBarcelonaSpain

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