`nonEq` — Non-equilibrium Markov model

Usage

nonEq(submodel: CTMC<a>, initialFreq: 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:: rate matrix; Default: nonRev
initialFreq:: Initial letter frequencies; Default: ~SymmetricDirichletOn(letters(a),1)
a:: The alphabet; Default: The alphabet in the current context

Original default expressions

initialFreq

~SymmetricDirichletOn(letters(@a),1)

a

get_state(alphabet)

A markov model with initial letter frequencies different from the equilibrium frequencies. Requires a rooted tree.

Note that even reversible models are directional if the initial frequencies are the equilibrium frequencues.

nonEq

GTR +> nonEq

nonRev +> nonEq

nonRev +> nonEq +> ASRV.Gamma(4) +> Inv