`GTR` — The General Time-Reversible rate matrix

Usage

GTR(sym: Map<String,Double>, pi: Map<String,Double>, a: a)
→ CTMC<a>

Arguments

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

sym:: Symmetric exchangability matrix; Default: ~SymmetricDirichletOn(letter_pairs(a),1)
pi:: Letter frequencies; Default: ~SymmetricDirichletOn(letters(a),1)
a:: The alphabet; Default: The alphabet in the current context

Original default expressions

sym

~SymmetricDirichletOn(letter_pairs(@a),1)

pi

~SymmetricDirichletOn(letters(@a),1)

a

get_state(alphabet)

Description

The general time-reversible rate matrix:

Q(i,j) = sym(i,j) * pi[j]

Examples

GTR({"AC":1,"AG":2,"AT":3,"CG":4,"CT":5,"GT":6},pi={"A":0.1,"C":0.2,"T":0.3,"G":0.4})

Citation

Tavare, Simon (1986). Some Probabilistic and Statistical Problems in the Analysis of DNA Sequences. Lectures on Mathematics in the Life Sciences 17: 57--86. Article