Sequence alignment

Pairwise and multiple alignment of biological sequences: Needleman–Wunsch and Smith–Waterman, affine gaps, banded, linear-space, semi-global and wavefront algorithms.

• Pairwise sequence alignment
• Banded sequence alignment
• Gotoh affine-gap alignment
• Hirschberg's linear-space alignment
• Multiple sequence alignment
• Pair hidden Markov models
• Profile hidden Markov models
• Semi-global and overlap alignment
• Smith–Waterman local alignment
• Wavefront alignment algorithm

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