`F81` — The Felsenstein (1981) rate matrix

Usage

F81(pi: Map<String,Double>, a: a)
→ CTMC<a>

Arguments

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

pi:: Letter frequencies; Default: ~SymmetricDirichletOn(letters(a),1.0)
a:: The alphabet; Default: The alphabet in the current context

Original default expressions

pi

~SymmetricDirichletOn(letters(@a),1.0)

a

get_state(alphabet)

Description

Rate matrix with equal exchangabilities, unequal frequencies.

Citation

Felsenstein, Joseph (1993). Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution 17(6): 368--376. DOI: 10.1007%2FBF01734359