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A web-based tool for PSI/TM-Coffee at The Centre for Genomic Regulation (CRG). The tool is specifically constructed to construct multiple sequence alignments (MSAs) of transmembrane proteins. It can use transmembrane databases for fast extension of homology.


Sequence analysis; Proteomics; Genomics


  • Operation: Multiple sequence alignment
  • Input: FASTA
  • Output: A graphical version of the MSA
  • Software interface: Web user interface; command-line user interface
  • Language: C++
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL v3
  • Cost: Free
  • Version name: -
  • Maturity: Mature
  • Credit: Plan Nacional [BFU2011-28575 to C.N., P.D.]; Center for Genomic Regulation (CRG); ‘Fundació Obra Social la Caixa’ (to E.W.F, M.C); Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017’ [SEV-2012–0208]; Center for Genomic Regulation (CRG).
  • Contact: cedric.notredame _at_
  • Collection: T-Coffee package


Floden EW, Tommaso PD, Chatzou M, Magis C, Notredame C, Chang JM "PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases." Nucleic Acids Res. 2016 Jul 8;44(W1):W339-43.
PMID: 27106060
PMCID: PMC4987888

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

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