R: Substitution Models for Mutation Processes

.substitution.model {phyclust} | R Documentation

## 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. | kappa, pi, t

Other models starting with `E_` use empirical frequencies for equilibrium probabilities.

### Author(s)

Wei-Chen Chen wccsnow@gmail.com

### 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

    ## End(Not run)

[Package phyclust version 0.1-30 Index]