For better experience, turn on JavaScript!



VerAlign is a web-based tool to compare two multiple sequence alignments (MSAs). It uses SPdist scoring scheme which measures a distance between mismatched amino acid pairs. Available from the Authors upon request.


Phylogeny; Sequence analysis; Nucleic acid sites, features and motifs; Nucleic acid structure analysis; Sequence sites, features and motifs


  • Operation: Multiple sequence alignment
  • Input: MSF; FASTA
  • Output: -
  • Software interface: Web user interface
  • Language: C
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Not stated
  • Cost: Free
  • Version name: -
  • Maturity: Stable
  • Credit: -
  • Contact: p.bawono _at_ | vsimoss _at_ | heringa _at_
  • Collection: -


Bawono P, van der Velde A, Abeln S, Heringa J "Quantifying the displacement of mismatches in multiple sequence alignment benchmarks." PLoS One. 2015 May 19;10(5):e0127431.
PMID: 25993129

Download and documentation

If you find errors, please report here.