Journal of Molecular Evolution

, Volume 33, Issue 2, pp 114–124

An evolutionary model for maximum likelihood alignment of DNA sequences

  • Jeffrey L. Thorne
  • Hirohisa Kishino
  • Joseph Felsenstein
Article

DOI: 10.1007/BF02193625

Cite this article as:
Thorne, J.L., Kishino, H. & Felsenstein, J. J Mol Evol (1991) 33: 114. doi:10.1007/BF02193625

Summary

Most algorithms for the alignment of biological sequences are not derived from an evolutionary model. Consequently, these alignment algorithms lack a strong statistical basis. A maximum likelihood method for the alignment of two DNA sequences is presented. This method is based upon a statistical model of DNA sequence evolution for which we have obtained explicit transition probabilities. The evolutionary model can also be used as the basis of procedures that estimate the evolutionary parameters relevant to a pair of unaligned DNA sequences. A parameter-estimation approach which takes into account all possible alignments between two sequences is introduced; the danger of estimating evolutionary parameters from a single alignment is discussed.

Key words

DNA sequence alignment Maximum likelihood procedure Dynamic programming Evolutionary model Insertion-deletion model 

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Copyright information

© Springer-Verlag New York Inc. 1991

Authors and Affiliations

  • Jeffrey L. Thorne
    • 1
  • Hirohisa Kishino
    • 1
  • Joseph Felsenstein
    • 1
  1. 1.Department of Genetics SK-50University of WashingtonSeattleUSA
  2. 2.Research Institute, University of TokyoTokyoJapan

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