Bioinformatics pp 507-535 | Cite as

Fixed-Parameter Algorithms in Phylogenetics

  • Jens Gramm
  • Arfst Nickelsen
  • Till Tantau
Part of the Methods in Molecular Biology™ book series (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.

Key words:

Phylogenetics perfect phylogeny fixed-parameter algorithms fixed-parameter tractable 

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Copyright information

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

Authors and Affiliations

  • Jens Gramm
    • 1
  • Arfst Nickelsen
    • 2
  • Till Tantau
    • 2
  1. 1.Wilhelm-Schickard-Institut für InformatikUniversität TübingenTübingenGermany
  2. 2.Institut für Theoretische InformatikUniversität zu LübeckLübeckGermany

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