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SHRiMP is a an aligner from the University of Toronto which uses a vectored Smith-Waterman for alignment. Although it is very slow, it detects alignments with high sensitivity and accuracy. It supports color space data.
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Fourierseq - current version: 2.02.1 (updated 11/14/11).
User documentation
- To get started using SHRiMP, read through the the SHRiMP documentation.
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