Installing other application in sub folder

I have a wordpress installation as the “root” installation of domain, that is I reach it directly by the url http://www.example.com/

Now I’m considering to adding a wiki, pmwiki, to the domain. Ideally I would like to add it as a sub-folder so I can reach it like this: http://www.example.com/wiki/

I tried this but since I’m using clean urls on the installation WP tries to interpret the ‘wiki’ part and tells me there is no such page.

Is it a very bad idea trying to do this? If not, is there some way I can configure WP to forget about ‘wiki’ calls and just let it through to pmwiki?

I tried searching the docs but since I don’t know what to search for I didn’t find anything.