Bibliography

Bishop and Friday, 1985
Bishop, M. J. and Friday, A. E. (1985).
Evolutionary trees from nucleic acid and protein sequences.
Proceeding of the Royal Society of London, B 226:271-302.

Blaisdell, 1989
Blaisdell, B. E. (1989).
Average values of a dissimilarity measure not requiring sequence alignment are twice the averages of conventional mismatch counts requiring sequence alignment for a computer-generated model system.
J Mol Evol, 29(6):538-47.

Dayhoff et al., 1978
Dayhoff, M. O., Schwartz, R. M., and Orcutt, B. C. (1978).
A model of evolutionary change in protein.
Atlas of Protein Sequence and Structure, 5(3):345-352.

Dempster et al., 1977
Dempster, A., Laird, N., Rubin, D., et al. (1977).
Maximum likelihood from incomplete data via the EM algorithm.
Journal of the Royal Statistical Society, 39(1):1-38.

Edgar, 2004
Edgar, R. C. (2004).
Muscle: a multiple sequence alignment method with reduced time and space complexity.
BMC Bioinformatics, 5:113.

Efron, 1982
Efron, B. (1982).
The jackknife, the bootstrap and other resampling plans, volume 38.
SIAM.

Felsenstein, 1981
Felsenstein, J. (1981).
Evolutionary trees from DNA sequences: a maximum likelihood approach.
J Mol Evol, 17(6):368-376.

Felsenstein, 1985
Felsenstein, J. (1985).
Confidence limits on phylogenies: An approach using the bootstrap.
Journal of Molecular Evolution, 39:783-791.

Gentleman and Mullin, 1989
Gentleman, J. F. and Mullin, R. (1989).
The distribution of the frequency of occurrence of nucleotide subsequences, based on their overlap capability.
Biometrics, 45(1):35-52.

Guindon and Gascuel, 2003
Guindon, S. and Gascuel, O. (2003).
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood.
Systematic Biology, 52(5):696-704.

Hasegawa et al., 1985
Hasegawa, M., Kishino, H., and Yano, T. (1985).
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA.
Journal of Molecular Evolution, 22(2):160-174.

Höhl et al., 2007
Höhl, M., Rigoutsos, I., and Ragan, M. A. (2007).
Pattern-based phylogenetic distance estimation and tree reconstruction.
Evolutionary Bioinformatics, 2:0-0.

Jones et al., 1992
Jones, D., Taylor, W., and Thornton, J. (1992).
The rapid generation of mutation data matrices from protein sequences.
Computer Applications in the Biosciences (CABIOS), 8:275-282.

Jukes and Cantor, 1969
Jukes, T. and Cantor, C. (1969).
Mammalian Protein Metabolism, chapter Evolution of protein molecules, pages 21-32.
New York: Academic Press.

Kimura, 1980
Kimura, M. (1980).
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.
J Mol Evol, 16(2):111-120.

Michener and Sokal, 1957
Michener, C. and Sokal, R. (1957).
A quantitative approach to a problem in classification.
Evolution, 11:130-162.

Posada and Crandall, 1998
Posada and Crandall (1998).
Modeltest: testing the model of dna substitution.
Bioinformatics.

Saitou and Nei, 1987
Saitou, N. and Nei, M. (1987).
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Mol Biol Evol, 4(4):406-425.

Whelan and Goldman, 2001
Whelan, S. and Goldman, N. (2001).
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach.
Molecular Biology and Evolution, 18:691-699.

Yang, 1994a
Yang, Z. (1994a).
Estimating the pattern of nucleotide substitution.
Journal of Molecular Evolution, 39(1):105-111.

Yang, 1994b
Yang, Z. (1994b).
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods.
Journal of Molecular Evolution, 39(3):306-314.