Description Usage Arguments Details Value References See Also Examples
This function calculates the joint distribution array for K matched sequences.
1 | gn(theta, 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 |
merge2 |
(K-1) x 2 matrix describing the tree topology |
This function calculates the joint distribution array for a tree with K matched sequences. it uses the following functions– Pt, Fmatrix and Smatrix.
A 4^K array containing the joint distribution for the K edges
Lars Sommer Jermiin, Vivek Jayaswal, Faisal Ababneh, John Robinson (2008). Phylogenetic model evaluation. Bioinformatics, Volume 452 of the series Methods in Molecular Biology, 331-364.
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.
Fmatrix, Pt, Smatrix
1 2 3 4 5 |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.