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Reconstructing Optimal Phylogenetic Trees: A Challenge in Experimental Algorithmics

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Book cover Experimental Algorithmics

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2547))

Abstract

The benefits of experimental algorithmics and algorithm engineering need to be extended to applications in the computational sciences. In this paper, we present on one such application: the reconstruction of evolutionary histories (phylogenies) from molecular data such as DNA sequences. Our presentation is not a survey of past and current work in the area, but rather a discussion of what we see as some of the important challenges in experimental algorithmics that arise from computational phylogenetics. As motivational examples or examples of possible approaches, we briefly discuss two specific uses of algorithm engineering and of experimental algorithmics from our recent research. The first such use focused on speed: we reimplemented Sanko. and Blanchette’s breakpoint analysis and obtained a 200, 000-fold speedup for serial code and 108-fold speedup on a 512-processor supercluster. We report here on the techniques used in obtaining such a speedup. The second use focused on experimentation: we conducted an extensive study of quartet-based reconstruction algorithms within a parameter-rich simulation space, using several hundred CPU-years of computation. We report here on the challenges involved in designing, conducting, and assessing such a study.

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Author information

Authors and Affiliations

  1. Department of Computer Science, University of New Mexico, 87131, Albuquerque, NM, USA

    Bernard M. E. Moret

  2. Department of Computer Sciences, University of Texas, 78712, Austin, TX, USA

    Tandy Warnow

Authors
  1. Bernard M. E. Moret
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  2. Tandy Warnow
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Editor information

Editors and Affiliations

  1. Department of Computer Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong

    Rudolf Fleischer

  2. Department of Computer Science, University of New Mexico, Farris Engineering Bldg, 87131-1386, Albuquerque, NM, USA

    Bernard Moret

  3. Department of Computer Science, University of Aarhus, Bld. 540, Ny Munkegade, 8000, Aarhus C, Denmark

    Erik Meineche Schmidt

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© 2002 Springer-Verlag Berlin Heidelberg

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Moret, B.M.E., Warnow, T. (2002). Reconstructing Optimal Phylogenetic Trees: A Challenge in Experimental Algorithmics. In: Fleischer, R., Moret, B., Schmidt, E.M. (eds) Experimental Algorithmics. Lecture Notes in Computer Science, vol 2547. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-36383-1_8

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  • DOI: https://doi.org/10.1007/3-540-36383-1_8

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-00346-5

  • Online ISBN: 978-3-540-36383-5

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