Pairwise (Needleman–Wunsch/Smith–Waterman) or progressive multiple sequence alignment uses a compact JavaScript implementation inspired by MUSCLE (MUltiple Sequence Comparison by Log-Expectation).
The focus is on the core mechanics of alignment and visualisation.
The code includes functionality for automatically checking and correcting the orientation of DNA/protein sequences.
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. - Use standard one-letter alphabets (DNA/RNA or protein). Remove spaces, numbers, and unusual symbols when possible.
- Auto mode selects pairwise alignment for 1–2 sequences and multiple sequence alignment for 3+ sequences.
- The badge near "FASTA input" updates as sequences are detected.
- Gap open penalizes starting a gap; gap extend penalizes extending an existing gap.
- Penalties are typically negative numbers (e.g., -10 open, -1 extend). More negative values generally produce fewer/shorter gaps.
- Global aligns end-to-end (Needleman–Wunsch). Local finds best matching subregions (Smith–Waterman).
- Visual shows colored residues and a simple conservation line (
*for fully conserved non-gap positions,.otherwise). - FASTA and CLUSTAL provide plain text exports suitable for downstream tools.
- Use "Output block width" to control line wrapping for readability.
- Privacy: alignments run locally in JavaScript; sequences are not sent to a server by this page.
- Limitations: this is a compact, educational implementation inspired by MUSCLE; results may differ from full MUSCLE builds and other aligners.
- If you see unexpected output, try: (i) switching output format, (ii) simplifying characters in the input, or (iii) using different gap penalties.