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MBE Advance Access published online on August 16, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm160
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© The Author 2007. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Statistics of the Log-Det Estimator

T Massingham* and N Goldman{dagger}

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom, CB10 1SD

* tim.massingham{at}ebi.ac.uk

{dagger} goldman{at}ebi.ac.uk

Received for publication April 19, 2007. Revision received June 12, 2007. Revision received July 13, 2007. Accepted for publication July 21, 2007.

The log-det estimator is a measure of divergence (evolutionary distance) between sequences of biological characters, DNA or amino acids for example, and has been shown to be robust to biases in composition that can cause problems for other estimators. We provide a statistical framework to construct high-accuracy confidence intervals for log-det estimates, and compare the efficiency of the estimator to that of maximum likelihood using time-reversible Markov models. The log-det estimator is found to have good statistical properties under such general models.

Key Words: log-det distance • pairwise distances • statistical properties


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