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.
.substitution.modelA data frame contains two character vectors, mode and code.type.
Wei-Chen Chen wccsnow@gmail.com
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.
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
.show.option,
.code.type,
.identifier,
.EMControl,
phyclust.
if (FALSE) {
library(phyclust, quiet = TRUE)
.substitution.model
}
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