For any weighted directed path-cycle graphs, a and b (referred to as structures), and any equal costs of operations (intermergings and duplication), we obtain an algorithm which, by successively applying these operations to a, outputs b if the first structure contains no paralogs (i.e., edges with a repeated name) and the second has no more than two paralogs for each edge. In finding the shortest sequence of operations to be applied to pass from a to b, the algorithm has a multiplicative error of at most 13/9 + ε, where ε is any strictly positive number, and its runtime is of the order of nO(ε−2.6), where n is the size of the input pair of graphs. In the case of no paralogs, equal sets of names in the structures, and equal operation costs, we have considered the following conditions on the transformation of a into b: all structures in them are from one cycle; all structures are from one path; all structures are from paths. For each of the conditions, we have obtained an exact (i.e., zero-error) quadratic time algorithm for finding the shortest transformation of a into b. For another list of operations (join and cut of a vertex, and deletion and insertion of an edge) over structures and for arbitrary costs of these operations, we have obtained an algorithm for the extension of structures specified at the leaves of a tree onto its interior vertices. The algorithm is exact if the tree is a star—in this case, structures in the leaves may even have unequal sets of names or paralogs. The runtime of the algorithm is of the order of nΧ + n2log(n), where n is the number of names in the leaves, and Χ is an easily computable characteristic of the structures in the leaves. In the general case, a cubic time algorithm finds a locally minimal solution.