SMMSA is a quick and easy tool for visualizing and formatting multiple sequence alignments. Because it runs in browser, it cannot handle very long sequences or too many sequences.
- Upload or paste aligned FASTA. The sequence type is automatically chosen, but check just in case.
- Increase the Alignment Width for longer lines.
- Change colors by CSS color names or HEX codes.
- Enable semimatches for additional coloring for transition mutations or mutations of similar amino acids.
- The Reference # is used to compare other sequences against a selected reference. For example, input 0 if you want to compare all sequences
against the first.
- Click on sequence names in the output alignment to change them.
- The Detail View gives details on sequence lengths, number of mismatches, and number of semimatches.
- The output can be pasted as formatted text into a Word document, or other rich-text application.
