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Fixed-Parameter Algorithms in Phylogenetics

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Bioinformatics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 452))

Abstract

This chapter surveys the use of fixed-parameter algorithms in phylogenetics. A central computational problem in this field is the construction of a likely phylogeny (genealogical tree) for a set of species based on observed differences in the phenotype, differences in the genotype, or given partial phylogenies. Ideally, one would like to construct so-called perfect phylogenies, which arise from an elementary evolutionary model, but in practice one must often be content with phylogenies whose “distance from perfection” is as small as possible. The computation of phylogenies also has applications in seemingly unrelated areas such as genomic sequencing and finding and understanding genes. The numerous computational problems arising in phylogenetics are often NP-complete, but for many natural parametrizations they can be solved using fixed-parameter algorithms.

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Author information

Authors and Affiliations

  1. Wilhelm-Schickard-Institut für Informatik, Universität Tübingen, Tübingen, Germany

    Jens Gramm

  2. Institut für Theoretische Informatik, Universität zu Lübeck, Lübeck, Germany

    Arfst Nickelsen & Till Tantau

Authors
  1. Jens Gramm
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  2. Arfst Nickelsen
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  3. Till Tantau
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Editor information

Editors and Affiliations

  1. School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia

    Jonathan M. Keith PhD

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© 2008 Humana Press, a part of Springer Science+Business Media, LLC

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Gramm, J., Nickelsen, A., Tantau, T. (2008). Fixed-Parameter Algorithms in Phylogenetics. In: Keith, J.M. (eds) Bioinformatics. Methods in Molecular Biology™, vol 452. Humana Press. https://doi.org/10.1007/978-1-60327-159-2_24

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  • DOI: https://doi.org/10.1007/978-1-60327-159-2_24

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-707-5

  • Online ISBN: 978-1-60327-159-2

  • eBook Packages: Springer Protocols

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