An overview of the wcd EST clustering tool.

Summary: The wcd system is an open source tool for clustering expressed sequence tags (EST) and other DNA and RNA sequences. wcd allows efficient all-versus-all comparison of ESTs using either the d2 distance function or edit distance, improving existing implementations of d2. It supports merging, refinement and reclustering of clusters. It is ‘drop in’ compatible with the StackPack clustering package. wcd supports parallelization under both shared memory and cluster architectures. It is distributed with an EMBOSS wrapper allowing wcd to be installed as part of an EMBOSS installation (and so provided by a web server). Availability: wcd is distributed under a GPL licence and is available from http://code.google.com/p/wcdest Contact: scott.hazelhurst@wits.ac.za Supplementary information: Additional experimental results. The wcd manual, a companion paper describing underlying algorithms, and all datasets used for experimentation can also be found at www.bioinf.wits.ac.za/∼scott/wcdsupp.html