Given trees T and To on the same taxon set, the transfer index φ(b,To) is the number of taxa that need to be ignored so that the bipartition induced by branch b in T is equal to some bipartition in To. Recently, Lemoine et al. [13] used the transfer index to design a novel bootstrap analysis technique that improves on Felsenstein’s bootstrap on large, noisy data sets. In this work, we propose an algorithm that computes the transfer index for all branches b ∈ T in O(n log3 n) time, which improves upon the current O(n2)-time algorithm by Lin, Rajan and Moret [14]. Our implementation is able to process pairs of trees with hundreds of thousands of taxa in minutes and considerably speeds up the method of Lemoine et al. on large data sets. We believe our algorithm can be useful for comparing large phylogenies, especially when some taxa are misplaced (e.g. due to horizontal gene transfer, recombination, or reconstruction errors).