A bug has been identified with the current SLiMSuite release when using BLAST+ to generate orthologue alignments with GOPHER. Sequences extracted from the blast database have the first letter of their name truncated. In real terms, this should not make a lot of difference (if using the recommended naming format) but it could present mapping issues. A few other programs, such as HAQESAC, may also be affected if BLAST+ is being used to extract sequences.
A fix is available on request and will be part of the next release, which should be soon.