gn function

Joint Distribution for K Matched Sequences

This function calculates the joint distribution array for K matched sequences.

gn(theta, merge2)

Arguments

• theta: a vector of variables containing the following parameters in this order--1. the first three parameters from $\pi_X$ vector, 2. the first three parameters from $\pi_Y$ vector, 3. the first three parameters from $f_0$ vector, 4. the six off-diagonal free parameters in the S matrix, 5. a scalar $\rho$, 6. a vector of lengths containing K-2 values
• merge2: (K-1) x 2 matrix describing the tree topology

Details

This function calculates the joint distribution array for a tree with K matched sequences. it uses the following functions-- Pt, Fmatrix and Smatrix.

Returns

A $4^K$ array containing the joint distribution for the K edges

References

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.

See Also

Fmatrix, Pt, Smatrix

Examples

#To generate a 4^5 gene array
merge2<-matrix(c(-1,-4,-3,2,-2,-5,1,3),4,2)
theta<-c(rep(.25,3), rep(.25,3), rep(.25,3), c(.2,.35,.79,.01,.93,.47), 3,.1,.5,.8)
gn.sec<-gn(theta, merge2)
gn.sec