For better experience, turn on JavaScript!



A creation of multiple alignments representing structural homology and evolutionary homology, require separate approaches. PRANK is designed for construction of multiple alignments reflecting the evolutionary homology and phylogenetic information to handle insertions and deletions.


Sequence analysis


  • Operation: Sequence comparison; Multiple sequence alignment
  • Input: FASTA
  • Output: FASTA; HSAML
  • Software interface: Command-line user interface
  • Language: C++
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL v2
  • Cost: Free
  • Version name: -
  • Credit: -
  • Contact: ari.loytynoja _at_
  • Collection: EBI Training Tools


Löytynoja A "Phylogeny-aware alignment with PRANK." Methods Mol. Biol. 2014;1079
PMID: 24170401

Download and documentation

If you find errors, please report here.