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A Memetic Algorithm for Phylogenetic Reconstruction with Maximum Parsimony

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Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBIO 2009)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 5483))

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Abstract

The Maximum Parsimony problem aims at reconstructing a phylogenetic tree from DNA, RNA or protein sequences while minimizing the number of evolutionary changes. Much work has been devoted by the research community to solve this NP-complete problem and many algorithms and techniques have been devised in order to find high quality solutions with reasonable computational resources. In this paper we present a memetic algorithm (implemented in the software Hydra) which is based on an integration of an effective local search operator with a specific topological tree crossover operator. We report computational results of Hydra on a set of 12 benchmark instances from the literature and demonstrate its effectiveness with respect to one of the most powerful software (TNT). We also study the behavior of the algorithm with respect to some fundamental ingredients.

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Author information

Authors and Affiliations

  1. University of Angers, LERIA, 2 Bd Lavoisier, 49045, Anger Cedex 01, France

    Jean-Michel Richer & Jin-Kao Hao

  2. LaBRI (UMR 5800) Université de Bordeaux, 351 cours de la Libération, 33405, Talence Cedex, France

    Adrien Goëffon

Authors
  1. Jean-Michel Richer
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  2. Adrien Goëffon
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  3. Jin-Kao Hao
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Editor information

Editors and Affiliations

  1. Italian National Research Council (CNR), Institute for High-Performance Computing and Networking (ICAR), Via P. Bucci 41C, 87036, Rende (CS), Italy

    Clara Pizzuti

  2. Center for Human Genetics Research Department of Molecular Physiology & Biophysics, Vanderbilt University, 519 Light Hall, TN 37232, Nashville, USA

    Marylyn D. Ritchie

  3. Department of Animal Production Epidemiology and Ecology, University of Torino, Via Leonardo da Vinci 44, 10095, Grugliasco, Italy

    Mario Giacobini

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© 2009 Springer-Verlag Berlin Heidelberg

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Richer, JM., Goëffon, A., Hao, JK. (2009). A Memetic Algorithm for Phylogenetic Reconstruction with Maximum Parsimony. In: Pizzuti, C., Ritchie, M.D., Giacobini, M. (eds) Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics. EvoBIO 2009. Lecture Notes in Computer Science, vol 5483. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-01184-9_15

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  • DOI: https://doi.org/10.1007/978-3-642-01184-9_15

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-01183-2

  • Online ISBN: 978-3-642-01184-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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