`TN93` — The Tamura-Nei (1993) nucleotide rate matrix

Usage

TN93(kappaPur: Double, kappaPyr: 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.

kappaPur:: A<->G Transition/transversion ratio; Default: ~LogNormal(log(2),0.25)
kappaPyr:: C<->T 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 Tamura-Nei model.

Citation

Tamura, Koichiro; Nei, Masatoshi (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.. Molecular biology and evolution 10(3): 512--526. DOI: 10.1093/oxfordjournals.molbev.a040023