Journal of Molecular Evolution

, Volume 34, Issue 1, pp 3–16 | Cite as

Inching toward reality: An improved likelihood model of sequence evolution

  • Jeffrey L. Thorne
  • Hirohisa Kishino
  • Joseph Felsenstein


Our previous evolutionary model is generalized to permit approximate treatment of multiple-base insertions and deletions as well as regional heterogeneity of substitution rates. Parameter estimation and alignment procedures that incorporate these generalizations are developed. Simulations are used to assess the accuracy of the parameter estimation procedure and an example of an inferred alignment is included.

Key words

Alignment Maximum likelihood procedure Dynamic programming Evolutionary model Insertion-deletion model 


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Copyright information

© Springer-Verlag New York Inc 1992

Authors and Affiliations

  • Jeffrey L. Thorne
    • 1
  • Hirohisa Kishino
    • 1
  • Joseph Felsenstein
    • 1
  1. 1.Department of Genetics SK-50University of WashingtonSeattleUSA

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