This function computes the Shimodaira--Hasegawa test for a set of trees.
sh.test(..., x, model = DNAmodel(), B = 100)
- either a series of objects of class
"phylo"separated by commas, or a list containing such objects.
- a list, a matrix, or a data frame containing the (aligned) DNA sequences.
- the model to be fitted to each tree (as an object of
- the number of bootstrap replicates.
The present implementation follows the original formulation of Shimodaira and Hasegawa (1999). A difference is that the bootstrap resampling is done on the original sequence data rather than the RELL method as sugested by Shimodaira and Hasegawa.
- a numeric vector with the P-value associated with each tree given in
Shimodaira, H. and Hasegawa, M. (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution, 16, 1114--1116.
data(woodmouse) t1 <- nj(dist.dna(woodmouse)) t2 <- rtree(15, tip.label = t1$tip.label) t3 <- rtree(15, tip.label = t1$tip.label) ### Are the NJ tree and two random tress significantly different? sh.test(t1, t2, t3, x = woodmouse, B = 100)