Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA)
algorithm (as described in 10.1093/bioinformatics/18.3.452) which is used to
generate consensus sequences. It supports three alignment modes: local
(Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment (overlap),
and three gap modes: linear, affine and convex (piecewise affine). It also
supports Intel SSE4.1+ and AVX2 vectorization (marginally faster due to high
latency shifts), SIMDe and dispatching.

WWW: https://github.com/rvaser/spoa