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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)

Abstract

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.

Keywords

Model Tree Substitution Rate Weighting Scheme Molecular Clock Combinatorial Weighting 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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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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