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Fast global sequence alignment for the masses!

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Global optimal sequence alignment using the Needleman-Wunsch algorithm.

Aligns DNA, RNA, protein sequence and more!

See our sister project local alignment using Smith-Waterman:

NeedlemanWunsch Web Site


  • Affine gap penalties
  • Can set no gap penalty for gaps at the beginning and end of alignments
  • Coloured ouput
  • Reads FASTA, FASTQ and plain sequence files (inc. gzip'ed files)
  • Preset DNA/Protein substitution matrices (PAM/BLOSUM etc)
  • Can load substitution penalty matrices
  • Portable C code that can be used in other bioinformatics projects

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Additional Project Details

Intended Audience

Education, Science/Research

User Interface

Command-line, Console/Terminal

Programming Language

C, C++


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