One of the major changes in the last release was the incorporation of BLAST+ as a replacement for BLAST. It should be noted that BLAST+ has not been benchmarked with SLiMSuite and it is not clear how and when it will behave differently, particularly with regards to UPC generation (i.e. generating clusters of unrelated proteins).
Early indications are that BLAST+ has a greater tendency to return no hits for short sequences. This can cause issues with SLiMSuite programs if
oldblast=F. This will be fixed in the next release but running with
dev=T gets round this issue in the meantime.
Please note that UPC may be different with BLAST versus BLAST+. This will need to be the focus of further study.