T-Coffee

T-Coffee is a multiple sequence alignment (MSA) program. It preprocesses 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.

Topic

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

Detail

  • Operation: Multiple sequence alignment

  • Software interface: Command-line user interface;web user interface

  • Language: C++

  • License: GNU GLP v3

  • Cost: Free

  • Version name: 12

  • Credit: Swiss National Science Foundation

  • Input: FASTA

  • Output: -

  • Contact: cedric.notredame@europe.com

  • Collection: T-Coffee

  • Maturity: Mature

Publications

  • T-Coffee: A novel method for fast and accurate multiple sequence alignment.
  • Notredame C, et al. T-Coffee: A novel method for fast and accurate multiple sequence alignment. T-Coffee: A novel method for fast and accurate multiple sequence alignment. 2000; 302:205-17. doi: 10.1006/jmbi.2000.4042
  • https://doi.org/10.1006/jmbi.2000.4042
  • PMID: 10964570
  • PMC: -
  • T-Coffee: Tree-based consistency objective function for alignment evaluation.
  • Magis C, et al. T-Coffee: Tree-based consistency objective function for alignment evaluation. T-Coffee: Tree-based consistency objective function for alignment evaluation. 2014; 1079:117-29. doi: 10.1007/978-1-62703-646-7_7
  • https://doi.org/10.1007/978-1-62703-646-7_7
  • PMID: 24170398
  • PMC: -
  • Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures.
  • Taly JF, et al. Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures. Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures. 2011; 6:1669-82. doi: 10.1038/nprot.2011.393
  • https://doi.org/10.1038/nprot.2011.393
  • PMID: 21979275
  • PMC: -

Download and documentation

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