Rev Language Reference
fndNdS - Add a dN/dS factor to a codon rate matrix.
Constructs a rate matrix on the 61 non-stop codons (in the standard genetic code).
Q(i,j) = Q'(i,j) * omega if aa(i) != aa(j)
* 1 if aa(i) == aa(j)
where aa(i) gives the amino acid for codon i in the standard genetic code, and
Q'(i,j) is the input rate matrix on codons.
The dNdS function can be used to construct other rate matrices in a modular fashion.
For example:
(i) MG94 = F81 + X3 + dNdS
(ii) MG94K = HKY85 + X3 + dNdS
Usage
fndNdS(RateMatrix submodel, RealPos omega)
Arguments
| submodel : | RateMatrix (pass by const reference) |
| Singlet (i.e. nucleotide) rate matrix. | |
| omega : | RealPos (pass by const reference) |
| The dN / dS rate ratio. |
Return Type
Example
kappa ~ dnLognormal(0,1)
omega ~ dnUniform(0,1)
nuc_pi ~ dnDirichlet( rep(2.0, 4) )
Q1 := fnCodonMG94K( kappa, omega, nuc_pi )
# This is the same.
Q2 := fndNdS(fnX3(fnHKY(kappa, nuc_pi)), omega) # HKY + X3 + dNdS,
# or HKY*3 + dNdS
er ~ dnDirichlet( v(1,1,1,1,1,1) )
Q3 := fndNdS(fnX3(fnGTR(er, nuc_pi)), omega) # GTR + X3 + dNdS
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