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T-Coffee

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

Details

  • Operation: Multiple sequence alignment
  • Input: FASTA
  • Output: -
  • 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_ europe.com
  • Collection: T-Coffee

Publications

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. https://doi.org/10.1006/jmbi.2000.4042
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. https://doi.org/10.1007/978-1-62703-646-7_7
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. https://doi.org/10.1038/nprot.2011.393
PMID: 21979275


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. https://doi.org/10.1007/978-1-62703-646-7_7
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. https://doi.org/10.1038/nprot.2011.393
PMID: 21979275


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