SNiPer can discover SNP candidate sites from CONTIGS produced by Phrap ace file.
If you use SNiPer, you shoud prepare one file that contains all EST names and their Cultivar (line) names.
We found 1,935 SNP site in 660 Unigenes by SNiPer.
The ace file from CAP3 would be also able to discover SNP site.

If you hope to use SNiPer, please mail to us.
We always and freely send the perl script and README if you are a researcher at an accademic institute.
If you are commercial reseacher, please tell me your research situation.