Description Usage Arguments Details Value References See Also Examples
This function generates random DNA samples using Rambaut and Grassly method.
1 | gn3sim(theta, seqLength, merge2)
|
theta |
a vector of variables containing the following parameters in this order–1. the first three parameters from π_X vector, 2. the first three parameters from π_Y vector, 3. the first three parameters from f_0 vector, 4. the six off-diagonal free parameters in the S matrix, 5. a scalar ρ, 6. a vector of lengths containing K-2 values |
seqLength |
the length of sequences we need to generate |
merge2 |
(K-1) x 2 matrix describing the tree topology |
This function generates a 4^K DNA array using Rambaut and Grassly, (1997) method. It depends on a set of variables theta, the sequence length and a merge matrix describing the tree topology.
A n x K observed divergence 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.
Ntml, simapp, simemb, gn, gn2, Fmatrix
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