STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time.
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AGREP - approximate GREP for fast fuzzy string searching. Files are searched for a string or regular expression, with approximate matching capabilities and user-definable records. Developed 1989-1991 by Udi Manber, Sun Wu et al. at the University of Arizona. ISC open source license since Sept. 2014.
ConStruct: Construction of RNA consensus structures.
tools for adding mutations to existing .bam files, used for testing mutation callers
Andreas Wilm's Github Pages