MD5 is known to be a bad algorithm

[Mikael]

MD5 has been shown to occasionally yield identical checksums for different files. Why not use SHA-512 instead?

[DV]

No hash is perfect, and MD5 collisions are rare (it's a lot better than CRC-32). That said, Duplicate Cleaner 2.0 does give the option of SHA and byte-to-byte algorithms.