Program/Resource	Website URL (accessed 1/13/2014)
perl	http://www.perl.org/get.html
python	http://www.python.org/download/
ssaha2	http://www.sanger.ac.uk/resources/software/ssaha2/
NCBI UniVec Core	ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec_Core
SolexaQA	http://solexaqa.sourceforge.net/
FastQC	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
khmer	https://github.com/ged-lab/khmer
Trinity	http://trinityrnaseq.sourceforge.net/
Trinity normalization script	http://trinityrnaseq.sourceforge.net/trinity_insilico_normalization.html
Assemblathon 2 evaluation scripts	https://github.com/ucdavis-bioinformatics/assemblathon2-analysis
BLAST+(which includes makeblastdb and blastx)	ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
linebreak	https://code.google.com/p/linebreak/
RSEM	http://deweylab.biostat.wisc.edu/rsem/
EdgeR User's Guide	http://www.bioconductor.org/packages/2.13/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
R	http://www.r-project.org/
EdgeR	http://www.bioconductor.org/packages/2.13/bioc/html/edgeR.html