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

  • Software interface: Web user interface; command-line user interface

  • Language: C++

  • License: GNU GLP v3

  • Cost: Free

  • Version name: -

  • Credit: -

  • Input: GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only)

  • Output: ClustalW, Pearson/FASTA, GCG MSF, Phylip, HTML

  • Contact: es-request@ebi.ac.uk

  • Collection: EBI Tools

  • Maturity: Mature



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