"infected with a botnet" could you expand on this more?
do you mean the website is running as part of the botnet,,,,
or it propagates the malware to spread the botnet?
if as part then could you listen for patterns with input/output? e.g. botnet C&C sends instructions and address/ip range, the site then acts on that.
chmod ---x--x--x,, i'm illiterate!