Smith Waterman Python Packages

pyopal

Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.

stride-align

SIMD-accelerated fuzzy string matching, sequence alignment (Smith-Waterman / Needleman-Wunsch), edit distance (Levenshtein / OSA / Indel / Jaro-Winkler), phonetic encoders (Soundex / Metaphone / NYSIIS / Caverphone), and Dynamic Time Warping — x86 / ARM / LoongArch / POWER kernels with first-class CJK.

minineedle

Needleman-Wunsch and Smith-Waterman algorithms in python

goombay

Python implementation of several sequence alignment algorithms such as Waterman-Smith-Beyer, Gotoh, and Needleman-Wunsch intended to calculate distance, show alignment, and display the underlying matrices.

pairwise-sequence-alignment

A Python module to calculate alignment between two sequences using EMBOSS' needle, stretcher, and water

gasal2-py

Python bindings for GASAL2 (GPU-accelerated pairwise alignment).