Download PAML

Transcript
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.