Increased accuracy in analytical molecular distance estimation
Analytical molecular distance estimates can be inaccurate and biased estimates of the total number of substitutions not only when the model of evolution they are based on is incorrect, but also when the method of estimating the total is too simple. This comes about because when there are different types of substitutions occurring simultaneously, it can become extremely difficult to estimate the number of the more quickly evolving type, and the variance of this larger number can overwhelm the total estimate. In this paper, in an extension of earlier work of \textit{K. Tamura} and \textit{M. Ney} [Mol. Biol. Evol. 10, 512-526 (1993)] with a simple two-parameter model of evolution, more accurate analytical distances are derived for models appropriate to a variety of known DNA types using generalized least squares principles of noise reduction. It is shown that the new estimates can be applied to achieve more accurate results for site-to-site rate variation, regions with biased nucleotide frequencies, and synonymous sites in protein-coding regions. This study also includes a methodology to obtain accurate distance estimates for large numbers of sequence regions evolving in different manners.
- Least squares estimation of molecular distance. Noise abatement in phylogenetic reconstruction
- Improved variance estimators for one- and two-parameter models of nucleotide substitution
- Improved Error Bounds for Genetic Distances from Dna Sequences
- Evolutionary distances corrected for purifying selection and ancestral polymorphisms
- Microsatellite behavior with range constraints: Parameter estimation and improved distances for use in phylogenetic reconstruction
- Improved variance estimators for one- and two-parameter models of nucleotide substitution
- Mathematical properties of some measures of evolutionary distance
- Pseudo-Reverse Approach in Genetic Evolution
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