An evolutionary model for maximum likelihood alignment of DNA sequences

  title={An evolutionary model for maximum likelihood alignment of DNA sequences},
  author={Jeffrey L. Thorne and Hirohisa Kishino and J. Felsenstein},
  journal={Journal of Molecular Evolution},
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… CONTINUE READING
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