`MultiFreq`

Usage

MultiFreq(submodel: Map<String,Double> ->
CTMC<a>, tree: Tree<t>, freqs: DiscreteDist<Map<String,Double>>,
nodeFreqs: IntMap<Map<String,Double>>,
n: Int, a: Alphabet) → CTMC<a>

Arguments

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

submodel:: The model to use on each branch; Default: |pi:GTR(pi=pi)|
tree:: The base model; Default: The tree in the current context
freqs:: The rate distribution; Default: ~DirichletMixture(SymmetricDirichletOn(letters(a),2),2,n)
nodeFreqs:: The frequencies for each node; Default: ~IIDMap(nodes(tree),freqs)
n:: The number of frequency components; Default: 2
a:: The alphabet; Default: The alphabet in the current context

Original default expressions

tree

get_state(tree)

freqs

~DirichletMixture(SymmetricDirichletOn(letters(@a),2),2,@n)

nodeFreqs

~IIDMap(nodes(@tree),@freqs)

a

get_state(alphabet)

Description

A non-equilibrium model where each node selects from a weighted collection of n frequences.

Examples

|pi:TN93(pi=pi)| +> MultiFreq(n=3) +> ASRV.Gamma