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Oxford University Press (OUP), Bioinformatics, 13(24), p. 1542-1546

DOI: 10.1093/bioinformatics/btn203

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An overview of the wcd EST clustering tool

Journal article published in 2008 by Scott Hazelhurst, Winston Hide ORCID, Zsuzsanna Lipták, Ramon Nogueira, Richard Starfield
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

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