phyclust (version 0.1-24)

.substitution.model: 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.model

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:

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: https://snoweye.github.io/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

# NOT RUN {
library(phyclust, quiet = TRUE)

.substitution.model
# }