More JABBA awards for bogus bioinformatics acronyms. These all come from a recent issue of Bioinformatics:

PEAR: a fast and accurate Illumina Paired-End reAd mergeR — if they allowed you to download two copies of a stripped down version of this tool, would that be a pair of pared PEARs?
SecStAnT: Secondary Structure Analysis Tool for data selection, statistics and models building — What is it with this trend towards using mixed-case for everything?
ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms — The title is not quite revealing the source of the acronym. The tool's name stems from Optimal Resolution of Multimapping Ambiguity of rNa-seq reads. Would ORMAR — or even ORMARR — have been such a terrible name?

Honorable mention:

orthAgogue: an agile tool for the rapid prediction of orthology relations — This is not an acronym or initialism, but I still have to ask...why is it just the 'A' that is upper case?