IBM Watson Research Center's Bioinformatics & Pattern Discovery Group has a number of interesting online tools (around a dozen in all) for which source code is available. Go to the Brief Tutorials page to get a quick idea of what the tools are all about. Some of them are rather esoteric, but by the same token that also means they're not the run-of-the-mill sequence analysis tools. These are IBM's own special contributions.
Worth checking out.
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