For better experience, turn on JavaScript!



A tool for multiple sequence alignment (MSA) using "form-and-polish strategy." The Authors claim OPAL to be more accurate than Muscle and similar to Muscle on protein sequence alignment and have similar accuracy as MAFFT and Muscle on DNA sequence alignments.


Sequence analysis


  • Operation: Multiple sequence alignment
  • Input: FASTA
  • Output: FASTA
  • Software interface: Command-line user interface
  • Language: Java
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Other
  • Cost: Free for noncommercial use
  • Version name: 2.1.3
  • Maturity: Stable
  • Credit: the University of Arizona National Science Foundation IGERT Genomics Initiative Grant DGE-0114420; The US National Science Foundation through Grant DBI-0317498.
  • Contact: Travis Wheeler opal _at_
  • Collection: -


Wheeler TJ, Kececioglu JD "Multiple alignment by aligning alignments." Bioinformatics. 2007 Jul 1;23(13):i559-68.
PMID: 17646343

Download and documentation

If you find errors, please report here.