Our CLIQS 1D Pro software is specifically designed for large scale gel-based datasets such as those used in RAPD: https://totallab.com/products/1d-band-matching-software/
It allows the user to build large databases of gel lane and band profiles and accurately match across them and compare results.
A free trial is available on our website to use with your own images if you want to test it's suitable for you or if you have any further questions, please feel free to reach out.