Abstract
The accuracy of quartet-puzzling method, which is widely used in molecular phylogenetic analysis depends heavily on the number of intermediate trees searched and the order of molecular sequences selected to generate these trees. Because the quality of intermediate trees cannot be guaranteed, the consensus results can easily be trapped into local optima. In this paper we present a new approach to guide the intermediate tree selection. Our experimental results show that the accuracy of reconstructed trees can be improved significantly. Using our method, the task can easily be partitioned into independent subtasks of different sizes. Therefore, it can effectively be implemented and run in the heterogeneous and dynamic environment of the computational grid.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Swofford, D.L., Olsen, G.J., Wadell, P.J., Hillis, D.M.: Chapter 11: Phylogenetic inference. In: hillis, D.M., Moritz, C., Mable, B.K. (eds.) Systematic Biology, Sinauer Associates Sunderland, Massachusetts
Williams, T.L., Moret, B.M.E.: An Investigation of Phylogenetic Likelihood Methods. In: Proceedings of the Third IEEE Symposium on BioInformatics and BioEngineering (BIBE 2003) (2003)
Strimmer, K., von Haeseler, A.: Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13(7), 964–969 (1996)
Schmidt, H.A., Strimmer, K., Vingron, M., von Haeseler, A.: TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18(3), 502–504 (2002)
Felsenstein, J.: Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368–376
Saitou, N., Nei, M.: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425 (1987)
Kluge, A.G., Farris, J.S.: Quantitative phyletics and the evolution of anurans. Syst. Zool. 18, 1–32 (1969)
Farris, J.S.: Methods for computing Wagner trees. Syst. Zool. 19, 83–92 (1970)
Rambaut, A.: Phylogenetic Tree Simulator Package Version 1.1 (2002), http://evolve.zoo.ox.ac.uk/software/phylogen/manual.php
Grassly, N.C., Adachi, J., Rambaut, A.: PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13, 559–560 (1997)
Robinson, D.R., Foulds, L.R.: Comparison of phylogenetic trees. Mathematical Biosciences 53, 131–147 (1981)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2004 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Wang, C., Zhou, B.B., Zomaya, A.Y. (2004). Quartet-Based Phylogenetic Inference: A Grid Approach. In: Cao, J., Yang, L.T., Guo, M., Lau, F. (eds) Parallel and Distributed Processing and Applications. ISPA 2004. Lecture Notes in Computer Science, vol 3358. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30566-8_47
Download citation
DOI: https://doi.org/10.1007/978-3-540-30566-8_47
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-24128-7
Online ISBN: 978-3-540-30566-8
eBook Packages: Computer ScienceComputer Science (R0)