Correlation matrices for the five core histone modification marks, 
sampled in regions corresponding to chromatin states relevant to those marks.
These matrices are stored in the 'correlation_matrices' directory, in the RData format.
Some concept code that can be used with these data:

mark <- "H3K4me1"; state <- 7; # example mark/state combination: H3K4me1 in the Enh state
load(paste("cor_", mark, "_", state, ".RData", sep=""));
d <- as.dist(1-markcor);
hclust_res <- hclust(d);
MDS_res <- cmdscale(d, eig=TRUE, k=nrow(markcor)-1);
# next: analyze and/or plot results

In addition to this, we also provide Newick formatted optimally ordered hierarchical trees,
annotated with bootstrap scores. These are available in the directory 'bootstrap_results'.