Description Usage Arguments Details Value References See Also Examples

This function calculates the symmetric matrix S.

1 | ```
Smatrix(s, pix)
``` |

`s` |
a vector of variables containing the six free parameters in the S matrix |

`pix` |
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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