seq-al

Aligning DNA and Protein sequences using Dynamic Programming

The following algorithms are implemented

1. Needleman-Wunsch Algorithm for global sequence alignment with linear gap penalties.
2. Modified Gotoh's Algorithm for global sequence alignment with affine gap penalties.
3. Smith-Waterman Algorithm for local sequence alignment with linear gap penalties.
4. Smith-Waterman Algorithm for local sequence alignment with affine gap penalties.

References:

1. Rolf Backofen (2010). Lecture Slides for Bioinformatics I — SS 2010. Institut für Informatik.
2. Flouri, T., Kobert, K., Rognes, T., & Stamatakis, A. (2015). Are all global alignment algorithms and implementations correct? BioRxiv.
3. Altschul, S. F., & Erickson, B. W. (1986). Optimal sequence alignment using affine gap costs. Bulletin of Mathematical Biology.