Trinity is an application for de novo reconstruction of transcriptomes from RNA-Seq data. Its home page is at http://trinityrnaseq.sourceforge.net/.
Trinity contains three applications - Inchworm, Chrysalis, and Butterfly. They are meant to be installed "in-tree". To install, just download Trinity from their website, untar it, and type 'make'.
There are two tests which come with Trinity:
The former tests the whole flow, and the latter tests Butterfly only.