TEST2 function

Test for Symmetry of Matched DNA Sequences

This function tests for symmetry between all the pairs of K matched DNA sequences.

TEST2(f)

Arguments

• f: a $4^K$ array containing the observed divergence array N

Details

This function calculates Bowker's test for symmetry, Stuart's test for marginal symmetry and the test for internal symmetry. It depends on the $4^K$ observed divergence array N.

Returns

A list of three lower triangle matrices - first: the lower triangle of the matrix contains (K-1) x (K-1) values shows Bowker's test between all the possible pairs of the K sequences

• second: the lower triangle of the matrix contains (K-1) x (K-1) values shows Stuart's test between all the possible pairs of the K sequences

• third: the lower triangle of the matrix contains (K-1) x (K-1) values shows the internal test between all the possible pairs of the K sequences

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

Ntml, simapp, simemb, TEST3

Examples

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)
F1<-gn(theta,merge2)
N1<-Ntml(1000,F1)
t2<-TEST2(N1)
t2