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R-Coffee is a package for multiple RNA sequence alignments, derived from T-Coffee package. It uses structural information in the construction of the sequence alignments and a special version of T-Coffee constructs the multiple sequence alignments incorporating the structural information. Requirements: RNAlpfold from the Vienna package, Mafft, Muscle, ProbCons, and ConSan.


Functional, regulatory and non-coding RNA; Nucleic acid structure analysis; Structure prediction; RNA; Sequence analysis


  • Operation: Pairwise sequence alignment; Multiple sequence alignment; Pairwise structure alignment; RNA secondary structure alignment
  • Input: FASTA
  • Output: -
  • Software interface: Web user interface
  • Language: C++
  • Operating system: Linux; Mac OS X
  • License: GNU GPL v3
  • Cost: Free
  • Version name: 12
  • Maturity: Mature
  • Credit: -
  • Contact: cedric.notredame _at_
  • Collection: T-Coffee


Wilm A, Higgins DG, Notredame C "R-Coffee: a method for multiple alignment of non-coding RNA." Nucleic Acids Res. 2008 May;36(9):e52.
PMID: 18420654
PMCID: PMC2396437

Moretti S, Wilm A, Higgins DG, Xenarios I, Notredame C "R-Coffee: a web server for accurately aligning noncoding RNA sequences." Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W10-3. doi: 10.1093/nar/gkn278. Epub 2008 May 15.
PMID: 18483080
PMCID: PMC2447777

Notredame C, Higgins DG, Heringa J "T-Coffee: A novel method for fast and accurate multiple sequence alignment." J Mol Biol. 2000 Sep 8;302(1):205-17.
PMID: 10964570

Magis C, Taly JF, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Notredame C "T-Coffee: Tree-based consistency objective function for alignment evaluation." Methods Mol Biol. 2014;1079:117-29.
PMID: 24170398

Taly JF, Magis C, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Kemena C, Notredame C "Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures." Nat Protoc. 2011 Nov;6(11):1669-82.
PMID: 21979275

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