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J Mol Evol. 1991 Aug;33(2):114-24.

An evolutionary model for maximum likelihood alignment of DNA sequences.

Author information

  • 1Department of Genetics, University of Washington, Seattle 98195.

Erratum in

  • J Mol Evol 1992 Jan;34(1):91.


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.

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