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Systematic Biology 2006 55(5):837-843; doi:10.1080/10635150600969880
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© 2006 Society of Systematic Biologists

Multipolar Consensus for Phylogenetic Trees

Cécile Bonnard, Vincent Berry and Nicolas Lartillot

Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier UMR 5506, CNRS-Université de Montpellier 2 161, rue Ada, 34392, Montpellier Cedex 5, France E-mail: lartillo{at}lirmm.fr (N.L.)

Edited by Roderic Page: Associate Editor


  Abstract

Collections of phylogenetic trees are usually summarized using consensus methods. These methods build a single tree, supposed to be representative of the collection. However, in the case of heterogeneous collections of trees, the resulting consensus may be poorly resolved (strict consensus, majority-rule consensus, ...), or may perform arbitrary choices among mutually incompatible clades, or splits (greedy consensus). Here, we propose an alternative method, which we call the multipolar consensus (MPC). Its aim is to display all the splits having a support above a predefined threshold, in a minimum number of consensus trees, or poles. We show that the problem is equivalent to a graph-coloring problem, and propose an implementation of the method. Finally, we apply the MPC to real data sets. Our results indicate that, typically, all the splits down to a weight of 10% can be displayed in no more than 4 trees. In addition, in some cases, biologically relevant secondary signals, which would not have been present in any of the classical consensus trees, are indeed captured by our method, indicating that the MPC provides a convenient exploratory method for phylogenetic analysis. The method was implemented in a package freely available at http://www.lirmm.fr/~cbonnard/MPC.html.

Keywords: Conciseness; consensus; graph-coloring; phylogeny; secondary signal

Received December 16, 2005; Revised February 21, 2006; Accepted May 2, 2006
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