`F` — The +F frequency model

Usage

F(submodel: ExchangeModel<a>, pi: Map<String,Double>, a: a)
→ CTMC<a>

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

submodel:: Symmetric (exchangability) matrix
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)

The +F frequency model species the rate matrix Q as:

Q(i,j) = s(i,j) * pi[j].

WAG +> F