RNA.M16A — Exchangability matrix on doublets constructed
from nucleotide exchange rates
Usage
RNA.M16A(aS: Double, aD: Double, b: Double, g: Double, e: 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.
-
aS: -
Exchange rate: 1 change, match <-> match
-
Default:
~LogNormal(log(2),0.25) -
aD: -
Exchange rate: 2 changes, match <-> match, both transitions
-
Default:
~LogNormal(log(2),0.25) -
b: -
Exchange rate: 2 changes, match <-> match, both transversions
-
Default:
~LogNormal(log(2),0.25) -
g: -
Exchange rate: 1 changes, match <-> mismatch
-
Default:
~LogNormal(log(2),0.25) -
e: -
Exchange rate: 1 changes, mismatch <-> mismatch
-
Default:
~LogNormal(log(2),0.25) -
a: -
The Doublets alphabet
-
Default: The alphabet in the current context
Original default expressions
-
pi -
~SymmetricDirichletOn(letters(@a),1) -
a -
get_state(alphabet)
Description
Exchangability matrix for rna stems that allows 2 simultaneous changes.
Note the exchange rate for double changes involving a mismatch is 0.
Examples
RNA.M16ARNA.M16A +> ASRV.FreeCitation
Savill, Nicholas J.; Hoyle, David C.; Higgs, Paul G. (2001). RNA Sequence Evolution With Secondary Structure Constraints: Comparison of Substitution Rate Models Using Maximum-Likelihood Methods. Genetics Society of America 157: 399--411. PMID: 11139520