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PAML MANUAL 61 11 References Adachi, J., and M. Hasegawa. 1996a. Model of amino acid substitution in proteins encoded by mitochondrial DNA. Journal of Molecular Evolution 42:459-468. Adachi, J., and M. Hasegawa. 1996b. MOLPHY Version 2.3: Programs for molecular phylogenetics based on maximum likelihood. Computer Science Monographs, 28:1-150. Institute of Statistical Mathematics, Tokyo. Anisimova, M., J. P. Bielawski, and Z. Yang. 2001. The accuracy and power of likelihood ratio tests to detect positive selection at amino acid sites. Molecular Biology and Evolution 18:1585-1592. Anisimova, M., J. P. Bielawski, and Z. Yang. 2002. Accuracy and power of Bayes prediction of amino acid sites under positive selection. Molecular Biology and Evolution 19:950-958. Anisimova, M., R. Nielsen, and Z. Yang. 2003. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164:1229-1236. Azzalini, A., and M. G. Genton. 2007. Robust likelihood methods based on the skew-t and related distributions. Int. Statist. Rev. 76:106-129. Bielawski, J. P., and Z. Yang. 2004. A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. Journal of Molecular Evolution 59:121-132. Bishop, M. J., and A. E. Friday. 1987. Tetropad relationships: the molecular evidence. Pp. 123-139 in C. Patterson, ed. Molecules and Morphology in Evolution: Conflict or Compromise? Cambridge University Press, Cambridge, England. Brown, W. M., E. M. Prager, A. Wang, and A. C. Wilson. 1982. Mitochondrial DNA sequences of primates: tempo and mode of evolution. Journal of Molecular Evolution 18:225-239. Chang, B. S., and M. J. Donoghue. 2000. Recreating ancestral proteins. Trends Ecol. Evol. 15:109114. Dayhoff, M. O., R. M. Schwartz, and B. C. Orcutt. 1978. A model of evolutionary change in proteins. Pp. 345-352. Atlas of protein sequence and structure, Vol 5, Suppl. 3. National Biomedical Research Foundation, Washington D. C. DeBry, R. W. 1992. The consistency of several phylogeny-inference methods under varying evolutionary rates. Molecular Biology and Evolution 9:537-551. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17:368-376. Felsenstein, J. 2004. Inferring Phylogenies. Sinauer Associates, Sunderland, Massachusetts. Felsenstein, J. 2005. Phylip: Phylogenetic inference program, Version 3.6. University of Washington, Seattle. Fitch, W. M. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 20:406-416. Forsberg, R., and F. B. Christiansen. 2003. A codon-based model of host-specific selection in parasites, with an application to the influenza A virus. Molecular Biology and Evolution 20:1252-1259. Galtier, N., and M. Gouy. 1998. Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Molecular Biology and Evolution 15:871-879.