Abstract
We study the convergence rates of neighbor-joining and several new phylogenetic reconstruction methods on families of trees of bounded diameter. Our study presents theoretically obtained convergence rates, as well as an empirical study based upon simulation of evolution on random birth-death trees. We find that the new phylogenetic methods offer an advantage over the neighbor-joining method, except at low rates of evolution where they have comparable performance. The improvement in performance of the new methods over neighbor-joining increases with the number of taxa and the rate of evolution.
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
K. Atteson. The performance of the neighbor-joining methods of phylogenetic reconstruction. Algorithmica, 25:251–278, 1999.
V. Berry and O. Gascuel. Inferring evolutionary trees with strong combinatorial evidence. In Proc. 3rd Ann. Int’l Conf. Computing and Combinatorics (COCOON 97), pages 111–123. Springer Verlag, 1997. in LNCS 1276.
M. Csűrös. Fast recovery of evolutionary trees with thousands of nodes. To appear in RECOMB 01, 2001.
M. Csűrös and M. Y. Kao. Recovering evolutionary trees through harmonic greedy triplets. Proceedings of ACM-SIAM Symposium on Discrete Algorithms (SODA 99), pages 261–270, 1999.
P. L. Erdos, M. Steel, L. Székély, and T. Warnow. A few logs suffice to build almost all trees-I. Random Structures and Algorithms, 14:153–184, 1997.
P. L. Erdos, M. Steel, L. Székély, and T. Warnow. A few logs suffice to build almost all trees-II. Theor. Comp. Sci., 221:77–118, 1999.
J. Huelsenbeck and D. Hillis. Success of phylogenetic methods in the four-taxon case. Syst. Biol., 42:247–264, 1993.
D. Huson, S. Nettles, and T. Warnow. Disk-covering, a fast-converging method for phylogenetic tree reconstruction. Comput. Biol., 6:369–386, 1999.
D. Huson, K. A. Smith, and T. Warnow. Correcting large distances for phylogenetic reconstruction. In Proceedings of the 3rd Workshop on Algorithms Engineering (WAE), 1999. London, England.
M. Kimura. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol., 16:111–120, 1980.
W.H. Li. Molecular Evolution. Sinauer, Massachuesetts, 1997.
C. McGeoch. Analyzing algorithms by simulation: variance reduction techniques and simulation speedups. ACM Comp. Surveys, 24:195–212, 1992.
B. Moret. Towards a discipline of experimental algorithmics, 2001. To appear in Monograph in Discrete Mathematics and Theoretical Computer Science; Also see http://www.cs.unm.edu/moret/dimacs.ps.
L. Nakhleh, U. Roshan, K St. John, J. Sun, and T. Warnow. Designing fast converging phylogenetic methods. Oxford U. Press, 2001. To appear in Bioinformatics: Proc. 9th Int’l Conf. on Intelligent Systems for Mol. Biol. (ISMB 01).
A. Rambaut and N. C. Grassly. Seq-gen: An application for the Monte Carlo simulation of dna sequence evolution along phylogenetic trees. Comp. Appl. Biosci., 13:235–238, 1997.
D. F. Robinson and L. R. Foulds. Comparison of phylogenetic trees. Mathematical Biosciences, 53:131–147, 1981.
M. Sanderson. r8s software package. Available from http://loco.ucdavis.edu/r8s/r8s.html.
N. Sautou and M. Nei. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4:406–425, 1987.
D. L. Swofford. PAUP*: Phylogenetic analysis using parsimony (and other methods), 1996. Sinauer Associates, Underland, Massachusetts, Version 4.0.
Condor Development Team. Condor high throughput computing program, Copyright 1990–2001. Developed at the Computer Sciences Department of the University of Wisconsin; http://www.cs.wisc.edu/condor.
T. Warnow, B. Moret, and K. St. John. Absolute convergence: true trees from short sequences. Proceedings of ACM-SIAM Symposium on Discrete Algorithms (SODA 01), pages 186–195, 2001.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2001 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Nakhleh, L., Roshan, U., John, K.S., Sun, J., Warnow, T. (2001). The Performance of Phylogenetic Methods on Trees of Bounded Diameter. In: Gascuel, O., Moret, B.M.E. (eds) Algorithms in Bioinformatics. WABI 2001. Lecture Notes in Computer Science, vol 2149. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-44696-6_17
Download citation
DOI: https://doi.org/10.1007/3-540-44696-6_17
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-42516-8
Online ISBN: 978-3-540-44696-5
eBook Packages: Springer Book Archive