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T-Coffee (EBI)

T-Coffee (EBI)

T-Coffee is a multiple sequence alignment (MSA) program. Web user interface and web services interfaces at EBI provides Simple Object Access Protocol (SOAP), Representational State Transfer (REST), Open API Interface, and Common Workflow Language (CWL) services. T-Coffee package pre-processes the data by making pair-wise alignments between all sequences and this information is incorporated in the progressive alignment procedure. The structural sequence information may be obtained from various different sources. It can align amino acid and nucleotide sequences. The package combines several alignment methods.


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


  • Operation: Multiple sequence alignment
  • Input: GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only)
  • Output: ClustalW, Pearson/FASTA, GCG MSF, Phylip, HTML
  • Software interface: Web user interface; command-line user interface
  • Language: C++
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GLP v3
  • Cost: Free
  • Version name: -
  • Maturity: Mature
  • Credit: -
  • Contact: es-request _at_
  • Collection: EBI Tools


Madeira F, Madhusoodanan N, Lee J, Tivey ARN, Lopez R "Using EMBL-EBI Services via Web Interface and Programmatically via Web Services." Curr Protoc Bioinformatics. 2019 Apr 30:e74.
PMID: 31039604

Harte N, Silventoinen V, Quevillon E, Robinson S, Kallio K, Fustero X, Patel P, Jokinen P, Lopez R "Public web-based services from the European Bioinformatics Institute." Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W3-9.
PMID: 15215339
PMCID: PMC441543

Pillai S, Silventoinen V, Kallio K, Senger M, Sobhany S, Tate J, Velankar S, Golovin A, Henrick K, Rice P, Stoehr P, Lopez R. "SOAP-based services provided by the European Bioinformatics Institute." Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W25-8.
PMID: 15980463
PMCID: PMC1160251

Labarga A, Valentin F, Anderson M, Lopez R. "Web services at the European bioinformatics institute." Nucleic Acids Res. 2007 Jul;35(Web Server issue):W6-11. Epub 2007 Jun 18.
PMID: 17576686
PMCID: PMC1933145

McWilliam H, Valentin F, Goujon M, Li W, Narayanasamy M, Martin J, Miyar T, Lopez R. "Web services at the European Bioinformatics Institute-2009." Nucleic Acids Res. 2009 Jul;37(Web Server issue):W6-10.
PMID: 19435877
PMCID: PMC2703973

Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J, Lopez R. "A new bioinformatics analysis tools framework at EMBL-EBI." Nucleic Acids Res. 2010 Jul;38(Web Server issue):W695-9.
PMID: 20439314
PMCID: PMC2896090

McWilliam H, Li W, Uludag M, Squizzato S, Park YM, Buso N, Cowley AP, Lopez R "Analysis Tool Web Services from the EMBL-EBI." Nucleic Acids Res. 2013 Jul;41(Web Server issue):W597-600.
PMID: 23671338
PMCID: PMC3692137

Li W, Cowley A, Uludag M, Gur T, McWilliam H, Squizzato S, Park YM, Buso N, Lopez R "The EMBL-EBI bioinformatics web and programmatic tools framework." Nucleic Acids Res. 2015 Jul 1;43(W1):W580-4.
PMID: 25845596
PMCID: PMC4489272

Chojnacki S, Cowley A, Lee J, Foix A, Lopez R "Programmatic access to bioinformatics tools from EMBL-EBI update: 2017." Nucleic Acids Res. 2017 Jul 3;45(W1):W550-W553.
PMID: 28431173
PMCID: PMC5570243

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