Skip to main content
Log in

On the maximum likelihood method in molecular phylogenetics

  • Published:
Journal of Molecular Evolution Aims and scope Submit manuscript


The efficiency of obtaining the correct tree by the maximum likelihood method (Felsenstein 1981) for inferring trees from DNA sequence data was compared with trees obtained by distance methods. It was shown that the maximum likelihood method is superior to distance methods in the efficiency particularly when the evolutionary rate differs among lineages.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others


  • Felsenstein J (1978) Cases in which parsimony and compatibility methods will be positively misleading. Syst Zool 27: 401–410

    Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    PubMed  Google Scholar 

  • Fukami-Kobayashi K, Tateno Y (1991) Robustness of maximum likelihood tree estimation against different patterns of base substitutions. J Mol Evol 32:79–91

    PubMed  Google Scholar 

  • Hasegawa M, Yano T (1984) Maximum likelihood method of phylogenetic inference from DNA sequence data. Bull Biomet Soc Japan 5:1–7

    Google Scholar 

  • Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism, vol III. Academic Press, New York, pp 21–132

    Google Scholar 

  • Saitou N (1988) Property and efficiency of the maximum likelihood method for molecular phylogeny. J Mol Evol 27:261–273

    PubMed  Google Scholar 

  • Saitou N, Imanishi T (1989) Relative efficiencies of the Fitch-Margoliash, maximum-parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree. Mol Biol Evol 6:514–525

    Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    PubMed  Google Scholar 

  • Sourdis J, Nei M (1988) Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree. Mol Biol Evol 5:298–311

    PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations


Rights and permissions

Reprints and permissions

About this article

Cite this article

Hasegawa, M., Kishino, H. & Saitou, N. On the maximum likelihood method in molecular phylogenetics. J Mol Evol 32, 443–445 (1991).

Download citation

  • Received:

  • Revised:

  • Issue Date:

  • DOI:

Key words