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Pro-Coffee is a part of the T_Coffee package and implemented for multiple sequence alignment of promoter regions.


Sequence analysis; DNA; Proteins; RNA


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


Erb I, González-Vallinas JR, Bussotti G, Blanco E, Eyras E, Notredame C "Use of ChIP-Seq data for the design of a multiple promoter-alignment method." Nucleic Acids Res. 2012 Apr;40(7):e52. doi: 10.1093/nar/gkr1292. Epub 2012 Jan 9.
PMID: 22230796
PMCID: PMC3326335

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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