Title: The role of internal node sequences and the molecular clock in the analysis of serially-sampled data

Authors: Patricia Buendia, Timothy M. Collins, Giri Narasimhan

Addresses: Department of Biology, Center for Computational Science, University of Miami, USA. ' Department of Biological Sciences, Florida International University, Miami, 33199 FL, USA. ' School of Computing and Information Science, Bioinformatics Research Group (BioRG), Florida International University, Miami, 33199 FL, USA

Abstract: Algorithms that infer phylogenetic relationships between serially-sampled sequences have been developed in recent years to assist in the analysis of rapidly-evolving human pathogens. Our study consisted of evaluating seven relevant methods using empirical as well as simulated data sets. In particular, we investigated how the molecular clock hypothesis affected their relative performance, as three of the algorithms that accept serially-sampled data as input assume a molecular clock. Our results show that the standard phylogenetic methods and MinPD had a better overall performance. Surprisingly, when all internal node sequences were included in the data, the topological performance measure of all the methods, with the exception of MinPD, dropped significantly.

Keywords: phylogenetics; serially-sampled data; molecular clock; experimental evolution studies; internal node sequences; viral evolution; bioinformatics; human pathogens.

DOI: 10.1504/IJBRA.2008.017167

International Journal of Bioinformatics Research and Applications, 2008 Vol.4 No.1, pp.107 - 121

Available online: 17 Feb 2008 *

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