Explaining why and how a tree t structurally differs from another tree t* is a question that is encountered throughout computer science, including in understanding tree-structured data such as XML or JSON data. In this article, we explore how to learn explanations for structural differences between pairs of trees from sample data: suppose we are given a set {(t1, t*1), . . ., (tn, t*n)} of pairs of labelled, ordered trees; is there a small set of rules that explains the structural differences between all pairs (ti, t*i)? This raises two research questions: (i) what is a good notion of “rule” in this context?; and (ii) how can sets of rules explaining a data set be learned algorithmically? We explore these questions from the perspective of database theory by (1) introducing a pattern-based specification language for tree transformations; (2) exploring the computational complexity of variants of the above algorithmic problem, e.g. showing NP-hardness for very restricted variants; and (3) discussing how to solve the problem for data from CS education research using SAT solvers.