Construction of molecular evolutionary phylogenetic trees from DNA sequences based on minimum complexity principle

Fengrong Ren, Hiroshi Tanaka*, Takashi Gojobori

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

Ever since the discovery of a molecular clock, many methods have been developed to reconstruct the molecular evolutionary phylogenetic trees. In this paper, we deal with the problem from the viewpoint of an inductive inference and apply Rissanen's minimum description length principle to extract the minimum complexity phylogenetic tree. Our method describes the complexity of the molecular phylogenetic tree by three terms which are related to the tree topology, the sum of the branch lengths and the difference between the model and the data measured by logarithmic likelihood. Five mitochondrial DNA sequences, from the human, the common chimpanzee, the pygmy chimpanzee, the gorilla and the orangutan, are used for investigating the validity of this method. It is suggested that this method might be superior to the traditional method in that it still shows good accuracy even near the root of phylogenetic trees.

Original languageEnglish (US)
Pages (from-to)121-130
Number of pages10
JournalComputer Methods and Programs in Biomedicine
Volume46
Issue number2
DOIs
StatePublished - Feb 1995
Externally publishedYes

Bibliographical note

Funding Information:
We thank Dr. Horai for providing us his mtDNA sequence data in machine readable format and Dr. Cheeseman for giving us an opportunity to read his papers on MDL. This research is partly supported by the National Institute of Genetics under a grant for collaboration study No. .56.

Keywords

  • Hominoidea
  • Maximum likelihood method
  • Minimum description length principle
  • Mitochondrial DNA sequence
  • Molecular evolutionary phylogenetic tree

ASJC Scopus subject areas

  • Software
  • Health Informatics
  • Computer Science Applications

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