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Maximum Parsimony Phylogenetic Inference Using Simulated Annealing

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EVOLVE - A Bridge between Probability, Set Oriented Numerics, and Evolutionary Computation II

Part of the book series: Advances in Intelligent Systems and Computing ((AISC,volume 175))

Abstract

The Maximum Parsimony (MP) problem aims at reconstructing a phylogenetic tree from DNA sequences while minimizing the total number of genetic transformations. In this paper we propose a carefully devised simulated annealing implementation, called SAMPARS (Simulated Annealing for Maximum PARSimony), for finding near-optimal solutions for the MP problem. Different possibilities for its key components and input parameter values were carefully analyzed and tunned in order to find the combination of them offering the best quality solutions to the problem at a reasonable computational effort. Its performance is investigated through extensive experimentation over well known benchmark instances showing that our SAMPARS algorithm is able to improve some previous best-known solutions.

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Author information

Authors and Affiliations

  1. LERIA, Université d’Angers, 2 Boulevard Lavoisier, 49045, Angers Cedex 01, France

    Jean-Michel Richer

  2. Information Technology Laboratory, CINVESTAV-Tamaulipas, Km. 5.5 Carretera Victoria-Soto La Marina, 87130, Victoria Tamps., Mexico

    Eduardo Rodriguez-Tello & Karla E. Vazquez-Ortiz

Authors
  1. Jean-Michel Richer
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  2. Eduardo Rodriguez-Tello
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  3. Karla E. Vazquez-Ortiz
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Corresponding author

Correspondence to Jean-Michel Richer .

Editor information

Editors and Affiliations

  1. , Computer Science Department, CINVESTAV-IPN, Col. San Pedro Zacatenco 2508, Mexico City, 07360, Mexico

    Oliver Schütze

  2. , Computer Science Department, CINVESTAV-IPN, Col. San Pedro Zacatenco 2508, Mexico City, 07360, Mexico

    Carlos A. Coello Coello

  3. , Computer Science and Communications, University of Luxembourg, rue Richard Coudenhove-Kalergi 6, Luxembourg, 1359, Luxembourg

    Alexandru-Adrian Tantar

  4. Computer Science and Communications, Research Unit, University of Luxembourg, rue Richard Coudenhove-Kalergi 6, Luxembourg, L-1359, Luxembourg

    Emilia Tantar

  5. Computer Science, and Communications, University of Luxembourg, rue Richard Coudenhove-Kalergi 6, Luxembourg, L-1359, Luxembourg

    Pascal Bouvry

  6. Bordeaux Mathematical Institute, INRIA Bordeaux-Sud Ouest, Université Bordeaux I, cours de la Libération 351, Talence Cedex, 33405, France

    Pierre Del Moral

  7. Bâtiment Leyteire, UFR Sciences et Modélisation, Université Bordeaux II, 3ter place de la Victoire, Bordeaux, 33000, France

    Pierrick Legrand

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Richer, JM., Rodriguez-Tello, E., Vazquez-Ortiz, K.E. (2013). Maximum Parsimony Phylogenetic Inference Using Simulated Annealing. In: Schütze, O., et al. EVOLVE - A Bridge between Probability, Set Oriented Numerics, and Evolutionary Computation II. Advances in Intelligent Systems and Computing, vol 175. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31519-0_12

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  • DOI: https://doi.org/10.1007/978-3-642-31519-0_12

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-31518-3

  • Online ISBN: 978-3-642-31519-0

  • eBook Packages: EngineeringEngineering (R0)

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