`F1x4` — F1x4 codon frequencies

Usage

F1x4(pi: Map<String,Double>, a: a)
→ Map<String,Double>

Type constraints: Triplets<a,b>

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

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

Original default expressions

pi

~SymmetricDirichletOn(letters(getNucleotides(@a)),1.0)

a

get_state(alphabet)

The F1x4 model describes codon frequencies pi' in terms of nucleotide frequencies pi:

pi'[ijk] = pi[i]*pi[l]*pi[k].

GY94(pi=F1x4)

F1x4(a=codons(DNA))