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Bibliography

Hasegawa, M. et al.
1985.
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA.
J. Mol. Evol., 42:160-174.

Hastings, W.
1970.
Monte carlo sampling methods using markov chains and their applications.
Biometrika, 57:97-109.

Higgs, P.
1998.
Compensatory neutral mutation and the evolution of RNA.
Genetica, 102:91-101.

Hudelot, C., V. Gowri-Shankar, H. Jow, M. Rattray, and P. Higgs
2003.
RNA-based phylogenetics methods: Application to mammalian mitochondrial RNA sequences.
Mol. Phyl. Evol.

Huelsenbeck, J., B. Larget, R. Miller, and F. Ronquist
2002.
Potential applications and pitfalls of bayesian inference of phylogeny.
Syst. Biol., 51(5):673-688.

Jow, H., C. Hudelot, M. Rattray, and P. Higgs
2002.
Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution.
Mol. Biol. Evol., 19(9):1591-1601.

Jukes, T. and C. Cantor
1969.
Evolution of protein molecules.
In Mammalian Protein Metabolism, volume 3, Pp.  21-132.
Munro, H.H., ed.

Kimura, M.
1980.
A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences.
J. Mol. Evol., 16:111-120.

Larget, B. and D. Simon
1999.
Markov chain monte carlo algorithms for the bayesian analysis of phylogenetic trees.
Molecular Biology and Evolution, 16(6):750-759.

Metropolis, N., A. Rosenbluth, M. Rosenbluth, A. Teller, and E. Teller
1953.
Equations of states calculations for fast computing machines.
Journal of Chemical Physics, 21:1087-1091.

Savill, N., D. Hoyle, and P. Higgs
2001.
Rna sequence evolution with secondary structure constraints: Comparison of substitution rate models using maximum likelyhood methods.
Genetics, 157:399-411.

Swofford, D. L., G. Olsen, P. Waddell, and D. Hillis
1996.
Phylogenetic inference.
In Molecular Systematics (2nd edition), Pp.  407-515.
Hillis, D.M.

Tamura, K. and M. Nei
1993.
Estimation of the number of nucleotide substitutions in the control region of mitochondrial dna in humans and chimpanzees.
Mol. Biol. Evol., 10(3):512-526.

Tillier, E. and R. Collins
1998.
High apparent rate of simultaneous compensatory basepair substitutions in ribosomal RNA.
Genetics, 148:1993-2002.

Tillier, E. R. M.
1994.
Maximum likelihood with multiparameter models of substitution.
Journal of Molecular Evolution, 39:409-417.

Whelan, S., P. Liò, and N. Goldman
2001.
Molecular phylogenetics: state-of-the art methods for looking into the past.
TRENDS in Genetics, 17(5):262-272.

Yang, Z.
1994.
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods.
J. Mol. Evol., 39:306-314.

Yang, Z.
1996.
Maximum likelihood models for combined analyses of multiple sequence data.
J. Mol. Evol., 42:587-596.



Gowri-Shankar Vivek 2003-04-24