MUSCLE-JS - Multiple Sequence Alignment

Pairwise (Needleman–Wunsch/Smith–Waterman) or progressive multiple sequence alignment uses a compact JavaScript implementation inspired by MUSCLE (MUltiple Sequence Comparison by Log-Expectation), focusing on core alignment mechanics and visualisation. The code includes functionality for automatically checking and correcting the orientation of DNA/RNA sequences. This is particularly important when working with sequenced data, where sequences may be in either the forward or reverse complementary orientation.

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Processed locally in your browser
FASTA input
Paste sequences below or load an example.
Input (FASTA)
Aligned output
Log / summary








  
  
       

        
      

      

        
      

      

        
      

      

        
      







  
Alignment Parameters

  

    

      

        
        
      

      

        
        
      

      

        
        
      

	        

        
        
      

      

        
        
      

    

  







  

    

      

        
Quick start

        

          1) Upload or paste FASTA  → 
          2) Set alignment type and gap penalties  → 
          3) Click Generate  → 
          4) Choose Visual, FASTA, or CLUSTAL output.
        

      

      
Recommended: Auto for routine use

    

  


  

    

      

        
      

      

        

          
    
            
  • FASTA headers start with >. Each header begins a new sequence record.
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  • Use standard one-letter alphabets (DNA/RNA or protein). Remove spaces, numbers, and unusual symbols when possible.
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  • Auto mode selects pairwise alignment for 1–2 sequences and multiple sequence alignment for 3+ sequences.
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  • The badge near “FASTA input” updates as sequences are detected.
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  • Gap open penalizes starting a gap; gap extend penalizes extending an existing gap.
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  • Penalties are typically negative numbers (e.g., -10 open, -1 extend). More negative values generally produce fewer/shorter gaps.
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  • Global aligns end-to-end (Needleman–Wunsch). Local finds best matching subregions (Smith–Waterman).
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  • Visual shows colored residues and a simple conservation line (* for fully conserved non-gap positions, . otherwise).
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  • FASTA and CLUSTAL provide plain text exports suitable for downstream tools.
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  • Use “Output block width” to control line wrapping for readability.
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  • Privacy: alignments run locally in JavaScript; sequences are not sent to a server by this page.
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  • Limitations: this is a compact, educational implementation inspired by MUSCLE; results may differ from full MUSCLE builds and other aligners.
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  • If you see unexpected output, try: (i) switching output format, (ii) simplifying characters in the input, or (iii) using different gap penalties.
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    Export: Click inside the output panel → Select all (Ctrl+A) → Copy (Ctrl+C) → Paste into your editor (Ctrl+V).
  


  

    Help: Input formats ·
    Help: Troubleshooting