AMD says its ROCm-enabled MMseqs2 and HIPSW++ tools move evolutionary sequence search onto Instinct GPUs, with up to 97 TCUPS in internal tests.

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. AMD said the two approaches address different parts of the workflow: HIPSW++ retains the exact dynamic-programming algorithm, and MMseqs2 uses filtering to remove unlikely matches before more expensive alignment stages. The company said this matters because modern databases can contain hundreds of millions of proteins, making full pairwise alignment at scale computationally expensive.

AMD described HIPSW++ as using wavefront parallelism on AMD GPUs, with intermediate values kept in thread-local registers where possible and boundary values exchanged through wavefront shuffle instructions. It said substitution matrices are staged in Local Data Share to reduce bank conflicts. For MMseqs2, AMD said the ROCm-enabled implementation accelerates the gapless alignment filter, where each dynamic-programming cell depends only on its upper-left diagonal neighbor, enabling row-wise GPU execution. The company also said the implementation supports multi-GPU execution by splitting the sequence database across multiple AMD GPUs on the same server.

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