BIGSdb
Software for storing and analysing bacterial sequence data
...The system incorporates the capacity to define and identify any number of loci and genetic variants at those loci within the stored nucleotide sequences. These loci can be further organised into schemes for isolate characterisation or for evolutionary or functional analyses.
See Jolley and Maiden 2010, BMC Bioinformatics 11:595 (http://www.biomedcentral.com/1471-2105/11/595).
You can report bugs or make enhancement requests using the issues tracker at https://github.com/kjolley/BIGSdb. The source code is also mirrored there.