AMD says MMseqs2 and HIPSW++ speed protein search on Instinct GPUs

AMD said it has built two open-source GPU paths for evolutionary sequence search on its Instinct hardware, positioning protein homology search and multiple sequence alignment on the same infrastructure used for downstream folding workloads. In a technical article published Oct. 14, 2026, the company said the tools are designed to accelerate an upstream step that often determines how much biological signal is available to AI models. According to AMD, HIPSW++ is a GPU implementation of exact SmithadWaterman alignment with affine gap penalties, while ROCm-enabled MMseqs2-GPU is intended for high-throughput homology search and MSA generation.

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