Your program is fantastic. Many thanks!!
I just prepared a Debian package for it and I such hope to spread
the news of your work to the community.
The link to a nice SNP selection program is of uttermost
importance. I very much appreciate that you have addressed this
issue. Also I am very happy to see the link to EnsEMBL to be
established. This is _very_ helpful and I wished you would also
allow to blast against EnsEMBL. Actually, maybe my institute will
be in the position to help with this in not too far future.
To be nice you could store the specification in an output that
Primer3 understands and you could also read the input of
Primer3. This is only to help users migrate to your work.
Another nice thing I have seen is the follow sf project "mipe"
which defines an XML standard to specify SNPs. You might want
to consider to support this.
Many thanks again