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Molecular Biology and Evolution, Vol 10, 1396-1401, Copyright © 1993 by Society for Molecular Biology and Evolution

ORIGINAL ARTICLE

Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites

Z Yang
Department of Animal Science, Beijing Agricultural University.

Felsenstein's maximum-likelihood approach for inferring phylogeny from DNA sequences assumes that the rate of nucleotide substitution is constant over different nucleotide sites. This assumption is sometimes unrealistic, as has been revealed by analysis of real sequence data. In the present paper Felsenstein's method is extended to the case where substitution rates over sites are described by the gamma distribution. A numerical example is presented to show that the method fits the data better than do previous models.
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