public domain smith-waterman (& some of them have needleman-wunsch) algorithm scripts which can be used as a module in your own applications.
Check test/README.md and whether the codes are working propery.
(I'm not familiar with GPU programming.)
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Public domain smith-waterman algorithm scripts (perl, python, Java, Rust, Rust+OpenCL, and JavaScript)
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yamule/smithwaterman
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Public domain smith-waterman algorithm scripts (perl, python, Java, Rust, Rust+OpenCL, and JavaScript)
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