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Theodore is a tool for semi-automated hybrid assembly of genomes, improving assembly quality by combining multiple information sources.

This collection of tools forms the basis of a pipeline for the complete enumeration of the number of solutions present in a model that maximizes a single objective function.

ExonFinder provides a pipeline to extract novel cassette exons and novel retained-introns from the results of mapping cross-species ESTs against a target genome via blat.

This is an approach that complements previous methods for reliable homozygous structural variation identification. Our approach accurately determines genotype and breakpoints relative to a reference genome based on de novo assembly of Illumina Genome Analyzer sequencing data. In this method, we examined only homozygous structural variations because detecting heterozygous structural variations requires assembly of haplotype sequences, which is not yet possible using existing assemblers.

SIPeS - Site Identification from Paired-end Sequencing

AQUA is a suite of programs for Analyzing the QUAlity of biomolecular structures that were determined via NMR spectroscopy. AQUA was developed by Ton Rullmann and Jurgen Doreleijers in the NMR Spectroscopy Department, Utrecht.