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.
Upload local FASTA file
— plain FASTA, multi-FASTA, or sequences
Alignment Parameters
Need details? Input format, scoring and gap penalties, output formats and the suggested workflow are documented in Help: MSA tool · Help: Troubleshooting
Exporting results: use Copy or Save view, or click inside the output box and select with the mouse.
Exporting results: use Copy or Save view, or click inside the output box and select with the mouse.