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
J. Adachi and M. Hasegawa. PROTML (maximum likelihood inference of protein phylogeny), 1995.
M. A. Beaumont and B. Rannala. The Bayesian revolution in genetics. Nature Review Genetics, 5:251–261, 2004.
G. Casella and R. L. Berger. Statistical Inference. Wadsworth & Brooks/Cole, Pacific Grove, CA, 1990.
B. Chor, M. D. Hendy, B. R. Holland, and D. Penny. Multiple maxima of likelihood in phylogenetic trees: An analytical approach. Molecular Biology and Evolution, 17:1529–1541, 2000.
B. Chor, M. D. Hendy, and D. Penny. Analytic solutions for three-taxon MLMC trees with variable rates across sites. In O. Gascuel and B. M. E. Moret, editors, Algorithms in Bioinformatics: First International Workshop, WABI 2001, Aarhus, Denmark, August 28-31, 2001, Proceedings, pages 204–214. Springer Verlag, Heidelberg, 2001.
B. Chor, A. Khetan, and S. Snir. Maximum likelihood on four taxa phylogenetic trees: Analytic solutions. In RECOMB, to appear, 2003.
A. W. F. Edwards. Likelihood. Cambridge University Press, Cambridge, expanded edition.
B. Efron and R. J. Tibshirani. An Introduction to the Bootstrap. Chapman & Hall, New York and London, first edition, 1993.
J. Felsenstein. Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution, 17:368–376, 1981.
J. Felsenstein. PHYLIP (phylogeny inference package), 1993.
N. Goldman. Statistical tests of models of DNA substitution. Journal of Molecular Evolution, 36:182–198, 1993.
R. R. Hudson. Gene genealogies and the coalescent process. In D. J. Futuyma and J. Antonovics, editors, Oxford Surveys in Evolutionary Biology, volume 7, pages 1–43. Oxford University Press, Oxford, 1990.
T. H. Jukes and C. R. Cantor. Evolution of protein molecules. In H. N. Munro, editor, Mammalian Protein Metabolism, pages 21–132. Academic Press, New York, 1969.
E. L. Lehmann and G. Casella. Theory of Point Estimation. Springer-Verlag, New York, 1998.
M. Nordborg. Coalecent theory. In D. J. Balding, M. Bishop, and C. Cannings, editors, Handbook of Statistical Genetics. Oxford University Press, Chichester, 2001.
J. S. Rogers and D. L. Swofford. Multiple local maxima for likelihoods of a phylogenetic tree: A simulation study. Molecular Biology and Evolution, 16:1079–1085, 1999.
N. Saitou and M. Nei. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4:406–425, 1987.
M. Stephens. Inference under the coalescent. In D. J. Balding, M. Bishop, and C. Cannings, editors, Handbook of Statistical Genetics, pages 213–238. John Wiley & Sons, Chichester, 2001.
K. Strimmer and A. von Haeseler. Quartet puzzling: A quartet maximum-likelihood method for reconstructing three topologies. Molecular Biology and Evolution, 7:964–969, 1996.
D. L. Swofford. PAUP*. Phylogenetic analysis using parsimony (* and other methods), 1998.
S. Tavaré. Some probabilistic and statistical problems in the analysis of DNA sequences. In M. S. Waterman, editor, Some Mathematical Questions in Biology: DNA Sequence Analysis, pages 57–86. The American Mathematical Society, Providence, RI, 1986.
Z. Yang. Complexity of the simplest phylogenetic estimation problem. Proceedings of the Royal Society of London, Series B: Biological Sciences, 267:109–119, 2000.
E. Zuckerkandl and L. Pauling. Evolutionary divergence and convergence in proteins. In V. Bryson and H. J. Vogel, editors, Evolving Genes and Proteins, pages 97–166. Academic Press, New York, 1965.
Author information
Authors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer Science+Business Media, Inc.
About this chapter
Cite this chapter
Buschbom, J., von Haeseler, A. (2005). Introduction to Applications of the Likelihood Function in Molecular Evolution. In: Statistical Methods in Molecular Evolution. Statistics for Biology and Health. Springer, New York, NY. https://doi.org/10.1007/0-387-27733-1_2
Download citation
DOI: https://doi.org/10.1007/0-387-27733-1_2
Publisher Name: Springer, New York, NY
Print ISBN: 978-0-387-22333-9
Online ISBN: 978-0-387-27733-2
eBook Packages: Mathematics and StatisticsMathematics and Statistics (R0)