TSTA: Thread and SIMD-Based Trapezoidal Pairwise/Multiple Sequence Alignment Method

Abstracts The rapid advancements in sequencing length necessitate the adoption of increasingly efficient sequence alignment algorithms. The Needleman-Wunsch method introduces the foundational dynamic programming (DP) matrix calculation for global alignment, which evaluates the overall alignment of sequences. However, this method is known to be highly time-consuming. The proposed TSTA algorithm leverages both vector-level and thread-level parallelism to accelerate pairwise and multiple sequence alignments. Availability & Implementation Source code are available at https://github.com/bxskdh/TSTA .