SequenceAligner Documentation

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DOI

Overview

SequenceAligner is a lightweight C++ tool designed for the comparative alignment of biological sequences. It supports three classic algorithms:

  • Longest Common Subsequence (LCS): Identifies the longest sequence of characters that appear left-to-right (not necessarily contiguously) in both sequences.
  • Global Alignment (Needleman-Wunsch): Finds the best full-length alignment between two sequences using dynamic programming.
  • Local Alignment (Smith-Waterman): Identifies the highest scoring local subsequence alignment useful for identifying conserved motifs.

This tool is optimized for command-line use with FASTA inputs and outputs colorful visual feedback.

Command-Line Usage

Usage

./aligner --query <query.fasta> --target <target.fasta> --choice <1|2|3|4> [--mode dna|protein] [--outdir <directory>] [--verbose]

Where:

  • --query specifies the first input FASTA file.
  • --target specifies the second input FASTA file.

  • --choice selects the alignment method:

  • 1 = global

  • 2 = local
  • 3 = LCS
  • 4 = all methods
  • --mode (optional) sets scoring mode: dna (default) or protein.
  • --outdir (optional) sets the output directory (default is current directory).
  • --verbose (optional) enables progress and detailed output.

Please refer to API Documentation