Mathematical models to reconstruct phylogenetic trees under the minimum evolution criterion

  • Authors:

  • Daniele Catanzaro;Martine Labbé;Raffaele Pesenti;Juan-José Salazar-González

  • Affiliations:

  • Graphes et Optimisation Mathématique, Département d'Informatique, Université Libre de Bruxelles, Boulevard du Triomphe, CP 210-01, B-1050, Brussels, Belgium;Graphes et Optimisation Mathématique, Département d'Informatique, Université Libre de Bruxelles, Boulevard du Triomphe, CP 210-01, B-1050, Brussels, Belgium;Dipartimento di Matematica Applicata, Universitá Ca' Foscari, Dorsoduro 3246 - 30123, Venice, Italy;Departamento de Estadística, Investigación Operativa y Computación, Universidad de La Laguna, Av. Astrofísico Francisco Sánchez, 38271 La Laguna, Tenerife, Spain

  • Venue:
  • Networks - Special Issue on Trees
  • Year:
  • 2009

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Abstract

A basic problem in molecular biology is to rebuild phylogenetic trees (PT) from a set of DNA or protein sequences. Among different criteria used for this purpose, the minimum evolution criterion is an optimality based criterion aiming to rebuild PT characterized by a minimal length. This problem is known to be 𝒩𝒫-hard. We introduce in this article some mixed integer programming models, and we also study possible cuts and lower bounds for the optimal value. So far, the number of sequences that can be involved in optimal phylogenetic reconstruction is still limited to 10. © 2008 Wiley Periodicals, Inc. NETWORKS, 2009