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. Author manuscript; available in PMC: 2015 May 1.
Published in final edited form as: Methods. 2013 Oct 16;67(1):20–27. doi: 10.1016/j.ymeth.2013.10.004

Table 1.

ShortStack software dependencies

Software Version tested with ShortStack Description URL Reference
perl 5.10.0 General purpose high-level interpreted programming language http://www.perl.org N/A
samtools 1.1.19 Utilities for manipulation of alignments in SAM (Sequence Alignment/Map) format http://samtools.sourceforge.net/ [8]
RNALfold & RNAeval (ViennaRNA package) 1.8.x, 2.x.x Predicts locally stable RNA secondary structures http://www.tbi.univie.ac.at/RNA/ [7]
bowtie & bowtie-build 0.12.x-1.0.0 Fast, gap-free short read (e.g. <50 bp) aligner based on the Burrows-Wheeler transform http://sourceforge.net/projects/bowtie-bio/files/bowtie/ [9]
einverted (EMBOSS package) 6.5.7 Finds inverted repeats in DNA sequences http://emboss.sourceforge.net/ [10]