pwalign

pwalign performs pairwise sequence alignments by solving global, local, and overlap alignment problems and computing edit distances or alignment score matrices for sets of strings.

Key Features:

• pairwiseAlignment(): Solves Needleman-Wunsch global alignment, Smith-Waterman local alignment, and ends-free overlap alignment problems.
• stringDist(): Computes the Levenshtein edit distance or pairwise alignment score matrix for a set of strings.

Scientific Applications:

• Sequence comparison: Identifies optimal alignments between two biological sequences to assess similarity and evolutionary relationships.
• Distance matrix construction: Generates pairwise alignment score matrices or edit distances for multiple sequence analysis and clustering.

Methodology:

The package implements dynamic programming algorithms for pairwise sequence alignment, specifically Needleman-Wunsch for global alignment, Smith-Waterman for local alignment, and ends-free overlap alignment, along with Levenshtein edit distance calculation.