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FAMSA is designed to produce rapid multiple sequence alignment of large protein families. It first determines the longest common subsequences and has a unique way to compute gap costs. It proceeds progressively to add sequences into the alignments using a novel iterative approach. The Authors claim FAMSA to be superior to Clustal Omega and MAFFT. A GPU version is available.


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


  • Operation: Multiple sequence alignment
  • Input: FASTA
  • Output: FASTA
  • Software interface: Command-line user interface
  • Language: C++
  • Operating system: Linux; Mac OS X
  • License: GNU General Public License v3
  • Cost: Free for non-comercial use
  • Version name: 1.2
  • Maturity: Stable
  • Credit: -
  • Contact: sebastian.deorowicz _at_
  • Collection: -


Deorowicz S, Debudaj-Grabysz A, Gudys A "FAMSA: Fast and accurate multiple sequence alignment of huge protein families." Sci Rep. 2016 Sep 27;6:33964.
PMID: 27670777

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