Molecular Biology and Evolution, Vol 13, 1375-1383, Copyright © 1996 by Society for Molecular Biology and Evolution
X Gu and WH Li
The statistical properties of the paralinear and LogDet distances under
nonstationary nucleotide frequencies were studied. First, we developed
formulas for correcting the estimation biases of the paralinear and LogDet
distances, i.e., the bias-corrected distance is estimated by dc = d -
2var(d), where d and var(d) are the estimated distance and sampling
variance, respectively. The performances of these formulas and the formulas
for sampling variances were examined by computer simulation. Second, we
developed a method for estimating the variance- covariance matrix of
paralinear distances, so that statistical tests of DNA phylogenies can be
conducted in the nonstationary case. Third, a new LogDet-based method for
testing the molecular clock hypothesis was developed under nonstationary
nucleotide frequencies.
ORIGINAL ARTICLE
Bias-corrected paralinear and LogDet distances and tests of molecular clocks and phylogenies under nonstationary nucleotide frequencies
Human Genetics Center, University of Texas at Houston 20334, USA.
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