F3x4
Usage
F3x4(pi1: Map<String,Double>, pi2: Map<String,Double>, pi3: Map<String,Double>, a: a)
→ Map<String,Double>
Arguments
Underlined names in default expressions refer to other arguments. A
default beginning with ~ specifies a prior
distribution.
-
pi1: -
Nucleotide frequencies for position 1
-
Default:
~SymmetricDirichletOn(letters(getNucleotides(a)),1.0) -
pi2: -
Nucleotide frequencies for position 2
-
Default:
~SymmetricDirichletOn(letters(getNucleotides(a)),1.0) -
pi3: -
Nucleotide frequencies for position 3
-
Default:
~SymmetricDirichletOn(letters(getNucleotides(a)),1.0) -
a: -
The (codon) alphabet
-
Default: The alphabet in the current context
Original default expressions
-
pi1 -
~SymmetricDirichletOn(letters(getNucleotides(@a)),1.0) -
pi2 -
~SymmetricDirichletOn(letters(getNucleotides(@a)),1.0) -
pi3 -
~SymmetricDirichletOn(letters(getNucleotides(@a)),1.0) -
a -
get_state(alphabet)
Description
The F3x4 model describes codon frequencies pi' in terms of nucleotide frequencies pi1, pi2, and pi3:
pi'[ijk] = pi1[i]*pi2[l]*pi3[k].
Examples
GY94(pi=F3x4)F3x4(a=codons(DNA))