Memory management in phylogenetic tree pairwise distance calculations

I have a metametabolite dendrogram (FTICR-MS data) and I'm measuring the pairwise branch lengths to create a null using randomized distribution.I'm using Bob Danczak's script here, which uses cophenetic() to calc the pairwise distances, then running a for loop to calculate the random distributions. My input is a large list (phylo) of 46.1 MB. Rightfully so I am receiving the error: Error in dist.nodes(x) : tree too big but I really need to calculate these distances. What are some memory-managing techniques to circumvent this issue? I'm certain it's the package and not my computer (8 cores, 64G RAM) though I'm never 100% confident when it comes to computers!