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gotoh

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lignum-vitae / goombay

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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.

python distance smith-waterman needleman-wunsch python3 similarity jaro-winkler levenshtein-distance alignment longest-common-subsequence sequence-alignment hamming-distance jaro longest-common-substring shortest-common-supersequence gotoh hirschberg gotoh-algorithm ratcliff-obershelp waterman-smith-beyer
  • Updated Aug 28, 2025
  • Python

odoluca / Fast-NW-and-SW-Pairwise-alignment-using-numba-JIT

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This project includes Needleman-Wunsch and Smith-Waterman algorithms and their afine gap variations (Gotoh) written to work with Cython, PyPy and Numba. Numba JIT shows greater performance. For Best performance use gotoh_jit.py to get only the best score and use gotoh_jit_traceback to get the best alignment

python cython smith-waterman needleman-wunsch python-3-6 alignment protein-sequences numba dna-sequences pairwise pairwise-alignment pypy3 gotoh
  • Updated Sep 22, 2021
  • Python

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