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Ergatis is a web-based utility that is used to create, run, and monitor reusable computational analysis pipelines; I was a developer on this project at The Institute for Genomic Research/J. Craig Venter Institute from 2005 to 2008.
LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.