ViennaRNA package is obtained from http://www.tbi.univie.ac.at/RNA
The squid library is obtained from http://eddylab.org/software/squid/
Randfold is obtained from http://bioinformatics.psb.ugent.be/software/details/Randfold
Bowtie is obtained from http://sourceforge.net/projects/bowtie-bio/files/bowtie/

