More Reliable Phylogenies by Properly Weighted Nucleotide Substitutions

  • Michael Schöniger
  • Arndt von Haeseler
Conference paper
Part of the Studies in Classification, Data Analysis and Knowledge Organization book series (STUDIES CLASS)


The efficiency of the neighbor-joining method under a variety of substitution rates, transition-transversion biases and model trees is studied. If substitution rates vary considerably and the ratio of transitions and transversions is large, even a Kimura (1980) two-parameter correction cannot guarantee reconstruction of the model tree. We show that application of the combinatorial weighting method by Williams and Fitch (1990) together with the Jukes-Cantor (1969) correction significantly improves the efficiency of tree reconstructions for a wide range of evolutionary parameters. Advantages, as well as limitations, of this approach are discussed.


Model Tree Substitution Rate Weighting Scheme Molecular Clock Combinatorial Weighting 
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Copyright information

© Springer-Verlag Berlin · Heidelberg 1993

Authors and Affiliations

  • Michael Schöniger
    • 1
  • Arndt von Haeseler
    • 2
  1. 1.Theoretical ChemistryTechnical University MunichGarchingGermany
  2. 2.Institute for ZoologyUniversity of MunichMunich 2Germany

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