An information-based sequence distance and its application to whole mitochondrial genome phylogeny

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journal

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Author(s)

  • Ming Li
  • Jonathan H. Badger
  • Xin Chen
  • Paul Kearney
  • Haoyong Zhang

Related Research Unit(s)

Detail(s)

Original languageEnglish
Pages (from-to)149-154
Journal / PublicationBioinformatics
Volume17
Issue number2
StatePublished - 2001

Abstract

Motivation: Traditional sequence distances require an alignment and therefore are not directly applicable to the problem of whole genome phylogeny where events such as rearrangements make full length alignments impossible. We present a sequence distance that works on unaligned sequences using the information theoretical concept of Kolmogorov complexity and a program to estimate this distance. Results: We establish the mathematical foundations of our distance and illustrate its use by constructing a phylogeny of the Eutherian orders using complete unaligned mitochondrial genomes. This phylogeny is consistent with the commonly accepted one for the Eutherians. A second, larger mammalian dataset is also analyzed, yielding a phylogeny generally consistent with the commonly accepted one for the mammals.

Citation Format(s)

An information-based sequence distance and its application to whole mitochondrial genome phylogeny. / Li, Ming; Badger, Jonathan H.; Chen, Xin; Kwong, Sam; Kearney, Paul; Zhang, Haoyong.

In: Bioinformatics, Vol. 17, No. 2, 2001, p. 149-154.

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journal