Understanding the \emph{transcriptome} -- not only what
  an organism's genomic sequence is, but also which genes are active
  and when they are active is an important question for molecular
  biology. Expressed Sequence Tags (ESTs) are a technology used to
  explore the transcriptome. These are short fragments of DNA created
  in the laboratory from mRNA extracted from a cell. The key
  computional step in the processing is \emph{clustering}: putting all
  ESTs associated from the same RNA together. Accurate clustering is
  quadratic in average EST length and number of ESTs, which makes
  \naive algorithms infeasible for real data sets. The \wcd EST
  clustering system is an open source clustering system that provides
  efficient implementations of key distance measures, heuristics for
  speeding up clustering, a pre-clustering booster based on suffix
  arrays, as well as parallelised implementations based on MPI and
  Pthreads.