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Input sequence file (FASTA format)


Gap Open

Gap Extension



  • Feb 2011 update: eProbalign has been updated and is now faster for
    both protein and RNA data and more accurate for RNA. Parameters for
    RNA alignment were obtained by cross-validating on RFAM 9.1
    seed alignments based on published structure. The standalone code
    has been updated to version 1.4 and is available for download.
  • Jobs that run for more than 10 hours will be terminated.
  • For large datasets (> 100 sequences) we recommend the standalone
    PROBALIGN software for local installation, available here
  • Browsers using this website must be Java and JavaScript enabled.
  • Please cite S. Chikkagoudar, U. Roshan and D. R. Livesay, eProbalign:
    generation and manipulation of multiple sequence alignments using
    partition function posterior probabilities, Nucleic Acids Research, Vol 35,
    2007, W675-W677 (pdf)