A zip file with the source code to wclique is available here: wclique.zip (11Kb).
A short tutorial on how we use wclique to construct genetic maps is available here.
To compile wclique you (temporarily?) need the LEDA Library installed. This class library provides string, array and graph classes used in wclique. It looks like I can replace this with STL (the C++ Standard Template Library) instead, so look for a version that doesn't require LEDA soon. I've compiled wclique on a linux 2.0 system (Redhat 3.0.3) and a Solaris 2.4 system, both using g++ 2.7.2. Once I get LEDA replaced, wclique should compile on just about any C++ compiler, it doesn't do anything fancy.