Multi-sequence alignment

Paste a multi-FASTA file or several FASTA records into one box (each sequence starts with >header, or paste raw sequence blocks separated by headers). Click Align to build a progressive alignment: sequences merge one at a time using Needleman–Wunsch, with greedy nearest-neighbor ordering from the first record.

You need at least three sequences. For two sequences, use the pairwise aligner. Choose DNA or Protein before aligning. All processing runs in your browser.