DAWGPAWS is a suite of command line programs written in Perl that accelerates annotation of genes and transposable elements in plant genomes by automating the process of running annotation programs and facilitating combined evidence annotation curation.
I wrote it, and recommend it.
DAWGPAWS has now been published in the journal Plant Methods. The article is at http://www.plantmethods.com/content/5/1/8 The PubMed link is http://www.ncbi.nlm.nih.gov/pubmed/19545381
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