Rev Language Reference

fnF2x4 - The F2x4 doublet frequency model

This treats doublet frequencies as a product of independent nucleotide frequencies.

Usage

fnF2x4(Simplex baseFrequencies1, Simplex baseFrequencies2)

Arguments

baseFrequencies1 : Simplex (pass by const reference)
The stationary frequencies of the 1st nucleotide.
baseFrequencies2 : Simplex (pass by const reference)
The stationary frequencies of the 2nd nucleotide.

Return Type

Simplex

Example

# An RNA stem model with independent base frequencies (from fnF2x4),
# and simultaneous 2-nucleotide changes allows.
nuc_pi ~ dnDirichlet( v(2.0, 2.0, 2.0, 2.0) )
rna_stem_er ~ dnDirichlet( rep(1.0, 16*15/2) )
rna_stem_pi := fnF2x4(nuc_pi, nuc_pi)
Q := fnGTR(rna_stem_er, rna_stem_pi)

See Also

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