Suppose you start out with a distance matrix. With e.g. PHYLIP, you can use neighbor, kitsch and fitch to turn such matrix into a tree. However, how would you go about getting a bootstrapped tree from a distance matrix?
I don't have much experience with trees but by googling I see there is the pvclust package which takes as input a (distance) matrix and performs bootstrap on the cluster analysis:
pvclust is an R package for assessing the uncertainty in hierarchical cluster analysis. For each cluster in hierarchical clustering, quantities called p-values are calculated via multiscale bootstrap resampling. P-value of a cluster is a value between 0 and 1, which indicates how strong the cluster is supported by data.
Could it help?