Described is a method and system for comparing two XML documents, usually represented as two logical dependency trees, and providing their differences as a set of tree operations. The set of tree operations may be used to transform one tree to the other. A first phase constructs an XML tree of nodes for each file, and a second, link tree construction phase builds a tree of link objects that relate nodes in the left tree to nodes in the right tree. Construction of the link tree generally operates by mapping equal subtrees in the left and right trees to each other, linking mapped subtrees to each other, removing any crossing links, linking groups, and filling gaps in the link tree. A third output phase uses the link tree to write an output file, such as comprising an XML document of change (e.g., insert and delete) operations.