phyclust (version 0.1-11)

.substitution: Substitution Models for Mutation Processes

Description

An object stores substitution models for mutation processes for Continuous Time Markov Chain theory. This is a read-only object and the elemental order is followed in C.

Usage

.substitution

format

A data frame contains two character vectors, mode and code.type.

Details

This data frame indicates substitution models implemented in C.

• 'model': names of substitution models for mutations.
• 'code.type': code types of substitution models, either NUCLEOTIDE or SNP.

The major models are: lll{ Model Author and Publication Parameter JC69 Jukes and Cantor 1969. $t$ K80 Kimura 1980. $\kappa, t$ F81 Felsenstein 1981. $\pi, t$ HKY85 Hasegawa, Kishino, and Yano 1985. $\pi, \kappa, t$ } Other models starting with E_ use empirical frequencies for equilibrium probabilities.

References

Phylogenetic Clustering Website: http://thirteen-01.stat.iastate.edu/snoweye/phyclust/

Jukes, T. H. and Cantor, C. R. (1969) Evolution of Protein Molecules, Mammalian Protein Metabolism, 3, 21-132

Kimura, M. (1980) A Simple Method for Estimating Evolutionary Rates of Base Substitutions through Comparative Studies of Nucleotide Sequences, Journal of Molecular Evolution, 16, 111-120

Felsenstein, J. (1981) Evolutionary Trees from DNA Sequences: A Maximum Likelihood Approach, Journal of Molecular Evolution, 17, 368-376

Hasegawa, M. and 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

See Also

.show.option, .code.type, .identifier, .EMControl, phyclust.

Examples

.substitution