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Results from 2 programs

Hello all,
Very general question.
Is anyone aware of a program that would compare the results of 2 identical
programs and show the individual point deviations in an excel file.
Example--first program would be a best fit.
2nd program would be a final.

Programs would be identical in the sense that the theoretical point locations
would be the same in both programs, but the alignments would
be different in the first and 2nd programs.

Thanks to everyone for any help offered.