Alternative to Hamming distance for permutations
Finding the minimal distance is called the "Sorting By Translocation" problem. Part of an abstract from a paper:

"Given two signed multi-chromosomal genomes Pi and Gamma with the same gene set, the problem of sorting by translocations (SBT) is to find a shortest sequence of translocations transforming Pi to Gamma, where the length of the sequence is called the translocation distance between Pi and Gamma. In 1996, Hannenhalli gave the formula of the translocation distance for the first time, based on which an $O(n^3)$ algorithm for SBT was given. In 2005, Anne Bergeron et al. revisited this problem and gave an elementary proof for the formula of the translocation distance which leads to a new $O(n^3)$ algorithm for SBT."

What's called "translocation" here is called a transposition, i.e., a permutation of exactly two elements in a list, in traditional combinatorial language.