Rev Language Reference

fnTrN - The Tamura-Nei (1993) nucleotide rate matrix

The Tamura-Nei nucleotide rate matrix.

Aliases

  • fnTamuraNei

Usage

fnTrN(RealPos kappa1, RealPos kappa2, Simplex baseFrequencies)

Arguments

kappa1 : RealPos (pass by const reference)
The first transition rate (A<->G).
kappa2 : RealPos (pass by const reference)
The second transition rate (C<->T).
baseFrequencies : Simplex (pass by const reference)
The stationary frequencies of the states.
Default : [ 0.250, 0.250, 0.250, 0.250 ]

Return Type

RateMatrix

Example

kappaAG ~ dnLognormal(0,1)    # The purine transition rate
kappaCT ~ dnLognormal(0,1)    # The pyrimindine transition rate
pi ~ dnDirichlet( v(1,1,1,1) )
Q := fnTrN(kappaAT, kappaCT, ,pi)

See Also

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