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References for Deep Time RCN (Methods and Software)

1. Britton, T., Oxelman, B., Vinnersten, A., and Bremer, K. 2002. Phylogenetic dating with confidence intervals using mean path-lengths. Molecular Phylogenetics and Evolution 24: 58-65.
2. Felsenstein, J. 1995. PHYLIP (phylogeny inference package). Distributed by author, Department of Genetics, University of Washington, Seattle.
3. Goldman, N. 1993. Statistical tests of models of DNA substitution. Journal of Molecular Evolution 36:182--198.
4. Hillis, D. M., B. K. Mable and C. Moritz. 1996. Applications of molecular systematics: the state of the field and a look to the future. In: Molecular systematics (D. M. Hillis, C. Morritz and B. K. Mable, eds.), pp. 515--543. Sinauer, Sunderland, Massachusetts, USA, 2nd edition.
5. Huelsenbeck, J. P., B. Larget and D. L. Swofford. 2000. A compound Poisson process for relaxing the molecular clock. Genetics 154:1879--1892.
6. Huelsenbeck, J. P. and B. Rannala. 1997. Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276:227--232.
7. Huelsenbeck, J. P. and F. Ronquist. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17:754--755.
8. Jukes, T. H. and C. R. Cantor. 1969. Evolution of protein molecules. In: Mammalian Protein Metabolism III (H.~N. Munro, ed.), pp. 21--132. Academic Press, New York.
9. Kishino, H., J. L. Thorne and W. J. Bruno. 2001. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Molecular Biology and Evolution 18:352--361.
10. Rambaut, A. and N. C. Grassly. 1997. Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Computer Applications for Biosciences 13:235--238.
11. Rambaut, A. E. and L. D. Bromham. 1998. Estimating divergence dates from molecular sequences. Molecular Biology and Evolution 15:442--448.
12. Sanderson, M. J. 1998. Estimating rate and time in molecular phylogenies: beyond the molecular clock? In: Molecular systematics of plants II. DNA sequences (D. E. Soltis, P. S. Soltis and J. J. Doyle, eds.), pp. 242--264. Kluwer Academic, Boston.
13. Sanderson, M. J. 1997 A nonparametric approach to estimating divergence times in the absence of rate constancy. Molecular Biology and Evolution 14:1218-1231
14. Sanderson, M. J. 2002 Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology Evolution 19:101-109.
15. Swofford, D. L. 2002. PAUP* 4.0: Phylogenetic Analysis Using Parsimony (* and other methods). Sinauer Associates, Sunderland, Massachusetts.
16. Swofford, D. L., G. J. Olsen}, P. J. Waddell and D. M. Hillis. 1996. Phylogenetic inference. In: Molecular Systematics (D. M. Hillis, C. Moritz and B. K. Mable, eds.), pp. 407--514. Sinauer Associates, Sunderland, Massachusetts.
17. Thorne, J. L., H. Kishino and I. S. Painter. 1998. Estimating the rate of evolution of the rate of molecular evolution. Molecular Biology and Evolution 15:1647--1657.
18. Yang, Z. 1994. Maximum likelihood phylogenetic estimations from DNA sequences with variable rates over sites: approximate method. Journal of Molecular Evolution 39:306--314.
19. Yang, Z. 2000. Phylogenetic Analysis by Maximum Likelihood (PAML). University College London, London, England, 3.0 edition.
20. Yoder and Yang, 2000 Estimation of primate speciation dates using local molecular clocks. Molecular Biology and Evolution 17: 1081-1090.
21. Zuckerkandl, E. and L. Pauling. 1962. Molecular disease, evolution, and genetic heterogeneity. In: Horizons in Biochemistry (V. Bryson and H. J. Vogels, eds.), pp. 189--225. Academic Press, New York.
22. Zuckerkandl, E. and L. Pauling. 1965. Evolutionary divergence and convergence in proteins. In: Evolving genes and proteins (V. Bryson and H. J. Vogels, eds.), pp. 97--166. Academic Press, New York.

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