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Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences
(2006)BMC BioinformaticsBackground The estimation of the difference between two evolutionary distances within a triplet of homologs is a common operation that is used for example to determine which of two sequences is closer to a third one. The most accurate method is currently maximum likelihood over the entire triplet. However, this approach is relatively time consuming. Results We show that an alternative estimator, based on pairwise estimates and therefore ...Journal Article -
Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise
(2008)BMC Evolutionary BiologyBackground The estimation of a distance between two biological sequences is a fundamental process in molecular evolution. It is usually performed by maximum likelihood (ML) on characters aligned either pairwise or jointly in a multiple sequence alignment (MSA). Estimators for the covariance of pairs from an MSA are known, but we are not aware of any solution for cases of pairs aligned independently. In large-scale analyses, it may be too ...Journal Article