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PSI-Coffee is a part of the T-Coffe distribution and specifically designed for making multiple sequence alignments (MSAs) of alpha-helical transmembrane protein sequences. The Authors claim PSI-Coffee to be more accurate than MSAProbs, Kalign, PROMALS, MAFFT, ProbCons, and PRALINE.


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: clustalw; MSF; PIR; FASTA; PHYLIP; ASCII; HTML; PDF; PS
  • Software interface: Command-line user interface; web user interface
  • Language: C++
  • Operating system: Linux; Mac OS X
  • License: GNU GLP v3
  • Cost: Free
  • Version name: 12
  • Maturity: Mature
  • Credit: Swiss National Science Foundation
  • Contact: cedric.notredame _at_
  • Collection: T-Coffee


Chang JM, Di Tommaso P, Taly JF, Notredame C "Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee." BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S1.
PMID: 22536955

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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