The on-going benchmarking of QSLiMFinder has thrown up a couple of discoveries to date. The first is that, reassuringly, it appears to work. (More on this another time.) The second is that it is slow. Or, at least, it was slow.
Thankfully, the cause of its surprisingly slow performance (compared to SLiMFinder) has been tracked down and fixed. At the same time, a (related) potential memory issue with large query sequences has also been sorted out.
The underlying problem is unlikely to have had a large effect on the SLiM prediction itself, although this is currently under investigation. The last release of SLiMSuite was only last week and, as QSLiMFinder is not officially published and released yet, I will not be compiling a new download immediately to take advantage of the improvements. The revised code is available on request if anyone is using QSLiMFinder.