- PIMMS – pipeline for analysis of insertional mutants in bacteria.
- BLAST2MATRIX– – an easy to use PERL blast wrapper for comparing a series of query sequences to a group of local databases.
- Cluster Rank – compare and rank hierarchical clustering methods R code.Please cite Clifford et al Frontiers in Genetics 2011
- Intergenic.distance.2.clash – scripts to determine the potential overlap of regulatory units. Please cite Russell K, Hasenkamp S, Emes R, Horrocks P. BMC Genomics. 2013 Apr 19;14:267.
- NIMBL Numerical Identification of Methylation Biomarker ListsMATLAB code to quality control and prioritize differentially methylated markers from illumina infinium arrays. Please cite: Wessely F and Emes RD. Identification of DNA methylation biomarkers from Infinium arrays. Frontiers in Genetics 3:161 2012.
- Predict genes by Exonerate – Perl pipeline for prediction of genes based on Guy Slater’s Exonerate. As used in Brown et al. Characterisation of retroviruses in the horse genome and their transcriptional activity via transcriptome sequencing. Virology 2012 and Tarlinton et al. Characterisation of a group of endogenous gammaretroviruses in the canine genome. The Veterinary Journal in press 2012