Perl Python Tcl/Tk
NCBI BLAST (public domain)
CAP3 Sequence Assembly Program Copyright by Xiaoqiu Huang, Michigan Technological University
Primer3 program Copyright Whitehead Institute for Biomedical Research
Also you can download Primer3 here
Programs and scripts developed at UCD, R. Michelmore Lab
(all Perl/Python/Tcl-Tk scripts below are under GNU General Public License)
Note: this pipeline was designed by year 2003. Since that time a sligthly different approach and improved scripts were developed. You can check the current protocol of EST selection and SNP discovery here.