The wcd manual: EST clustering using d2

Scott Hazelhurst
School of Computer Science
University of the Witwatersrand


This manual describes @code{wcd} (pronounced `wicked'), a program that
performs d2-clustering. Essentially, it takes a set of DNA sequences
(typically Expressed Sequence Tags, ESTs), and clusters the sequences
into the related groups.

This manual assumes that a user understand the basic principles of what
EST clustering is about, and so the basic concepts are only briefly
reviewed in this chapter. Subsequent chapter discuss installing and
running @code{wcd}, as well as giving some technical background so
someone who wants to use some of the code.