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BMCBI
2006

Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences

8 years 11 months ago
Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences
Background: 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 much faster to compute, has almost the same statistical power as the maximum likelihood estimator. We also provide a numerical approximation for its variance, which could otherwise only be estimated through an expensive re-sampling approach such as bootstrapping. An extensive simulation demonstrates that the approximation delivers precise confidence intervals. To illustrate the possible applications of these results, we show how they improve the detection of asymmetric evolution, and the identification of the closest relative to a given sequence in a...
Christophe Dessimoz, Manuel Gil, Adrian Schneider,
Added 10 Dec 2010
Updated 10 Dec 2010
Type Journal
Year 2006
Where BMCBI
Authors Christophe Dessimoz, Manuel Gil, Adrian Schneider, Gaston H. Gonnet
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