I have seen two softwares that does what you wish. Chess Position Trainer is one of them. The other is bookup.
Those softwares reads games in pgn and files containing epd positions with its evaluations in centipawns. This files contains the leaf nodes positions, generated by Chess Position Trainer for instance. You later analyze the epd file.
I use "GradualTest ver. 2.6" for this purpose. This program feeds the positions to an engine and writes the results to another file. I import the resulting file and the evaluations are added at the leaf positions. Later, the program propagates the valuations to the upstream positions, up to the root, applying the minimax algorithm.
Both programs are the best I have seen.