Infer distance since duplication from tree?
Assuming a molecular clock, the distance between the sequences and the duplication event is 75/2 = 37.5. Ideally, these sequences should have the same distance from the internal node (under a clock), and you could use a model that explicitly assumes a clock -- which will lead to ultrametric trees.  One example is the program promlk (or dnamlk) from the phylip package. A faster alternative would be the  UPGMA method, which also gives you an ultrametric tree.