K-Estimator is a software that estimates the number of of synonymous (Ks) and nonsynonymous substitutions (Ka) per site (divergence) when comparing two aligned nucleotide sequences, both protein-coding and non-coding. Confidence intervals of the divergence estimates are obtained by Monte Carlo simulation.
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Comeron JM. (1999)
K-Estimator: calculation of the number of nucleotide substitutions per site and the confidence intervals.