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JAguc – A Software Package for Environmental Diversity Analyses

Dec 2011 (Written: Jun 2011)

Sebastian Wild, Markus Nebel, Michael Holzhauser, Lars Hüttenberger, Raphael Reitzig, Matthias Sperber, and Thorsten Stoeck:

Journal of Bioinformatics and Computational Biology (2011) 9 (6): 749-773

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This paper – and the software tool JAguc that it describes – was the outcome of a programming project that I did with Michael Holzhauser, Lars Hüttenberger, Raphael Reitzig and Matthias Sperber during by Bachelor’s studies. JAguc computes a hierarchical clustering of RNA sequences based on pairwise alignments (a generalized edit distance), where common prefixes of the sequences are exploited to speed up computation.

The tool has been in use for some years by biologists; partly for its intended purpose, partly as a convenient frontend for BLAST.