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BAliBASE (Benchmark Alignment dataBASE) is a multiple sequence alignment (MSA) benchmarking reference set. It contains reference alignments based on three-dimensional structures and particular reference sets that contain various linear motifs. The AUthors also provide a program that can compare a test alignment with the BAliBASE reference alignment.


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


  • Operation: Multiple sequence alignment
  • Software interface: Command-line user interface
  • Language: C
  • License: Not stated
  • Cost: Free
  • Version name: 4 / 9
  • Credit: -
  • Contact: Julie Thompson thompson _at_ | Raymond Ripp raymond.ripp _at_
  • Collection: -


Bahr A, Thompson JD, Thierry JC, Poch O "BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations." Nucleic Acids Res. 2001 Jan 1;29(1):323-6.
PMID: 11125126

Thompson JD, Koehl P, Ripp R, Poch O "BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark." Proteins. 2005 Oct 1;61(1):127-36.
PMID: 16044462

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