This function calculates the symmetric matrix S.
a vector of variables containing the six free parameters in the S matrix
a vector giving the stationary probabilities for the four nucleotides A, C, G and T
This function calculates the matrix S, which we used to calculate the rate matrix R.
A 4 x 4 symmetric matrix
Faisal Ababneh, Lars S Jermiin, Chunsheng Ma, John Robinson (2006). Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences. Bioinformatics, 22(10), 1225-1231.
Pt, Fmatrix, gn ,gn2
1 2 3 4
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