More Reliable Phylogenies by Properly Weighted Nucleotide Substitutions
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.
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