FAMSA

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.

Topic

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

Detail

  • Operation: Multiple sequence alignment

  • Software interface: Command-line user interface

  • Language: C++

  • License: GNU General Public License v3

  • Cost: Free for non-comercial use

  • Version name: 1.2

  • Credit: -

  • Input: FASTA

  • Output: FASTA

  • Contact: sebastian.deorowicz@polsl.pl

  • Collection: -

  • Maturity: Stable

Publications

  • FAMSA: Fast and accurate multiple sequence alignment of huge protein families.
  • Deorowicz S, et al. FAMSA: Fast and accurate multiple sequence alignment of huge protein families. FAMSA: Fast and accurate multiple sequence alignment of huge protein families. 2016; 6:33964. doi: 10.1038/srep33964
  • https://doi.org/10.1038/srep33964
  • PMID: 27670777
  • PMC: -

Download and documentation

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