Table 2. Overview of external programmes.
| Programme | Version |
|---|---|
| Blast | 2.2.29+ |
| BEDTools | 2.17.0 |
| Bowtie2 | 2.1.0 |
| Clustal Omega | 1.2.4 |
| Cufflinks | 2.1.1 |
| FastQC | 0.10.1 |
| Mcl | 14.137 |
| R | 3.0 and 3.1 |
| Ruby | 2.0 and 2.1 |
| SAMTools | 0.1.19 |
| TopHat2 | 2.0.11 |
| ViennaRNA | 2.1.8 |
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