`HKY85` — The Hasegawa-Kishino-Yano (1985) nucleotide rate matrix

Usage

HKY85(kappa: Double, pi: Map<String,Double>, a: a)
→ CTMC<a>

Type constraints: Nucleotides<a>

Arguments

Underlined names in default expressions refer to other arguments. A default beginning with ~ specifies a prior distribution.

kappa:: Transition/transversion ratio; Default: ~LogNormal(log(2),0.25)
pi:: Letter frequencies; Default: ~SymmetricDirichletOn(letters(a),1)
a:: The alphabet; Default: The alphabet in the current context

Original default expressions

pi

~SymmetricDirichletOn(letters(@a),1)

a

get_state(alphabet)

Description

The HKY85 model

Citation

Hasegawa, Masami; Kishino, Hirohisa; Yano, Taka-aki (1985). Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of molecular evolution 22(2): 160--174. DOI: 10.1007/BF02101694