How to "fingerprint" a file (cryptographic hash function)?

Question: I need to test if certain system files are being altered so I need to compare the before and after states. I read that MD5 and SHA-1 are popular ways to do the fingerprint but that they have flaws. Is there something better? Anyway which software can be used to create the hash?

Info:
By "fingerprinting" the system files immediately after a fresh system install and then again after any subsequent changes made to the system (e.g. installing new software), the user or administrator will be alerted to any dangerous changes to the system's files. In the fingerprinting process a cryptographic hash function is used to create a fixed-length number... By calculating and comparing hash values of files (the essence of the fingerprint)..changes not made by any intended user of the system can be detected.
http://en.wikipedia.org/wiki/rootkit#det...

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If you're so goddamn concerned about it...

Just install Tripwire.


If you take the time to properly secure your system... you won't need to worry about it.

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