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T-Coffee
Developer:Cédric Notredame, CNRS Information Génomique et Structurale
Latest release:5.05
OS:UNIX, Linux, MS-Windows
Genre:Bioinformatics tool
Licence:GPL
Website:http://www.tcoffee.org


T-Coffee (Tree-based Consistency Objective Function For alignment Evaluation) is a multiple sequence alignment software using a progressive approach. It generates a library of pairwise alignments to guide the multiple sequence alignment. It can also combine multiple sequences alignments obtained previously and in the latest versions can use structural information from PDB files (3D-Coffee). It has advanced features to evaluate the quality of the alignments and some capacity of identifying occurrence of motifs (Mocca). It produces alignment in the aln format (Clustal) by default, but can also produce PIR, MSF and FASTA format. The input files are always in FASTA format. Note that what T-Coffee terms "Clustal" format is sufficiently different from the output of ClustalW/X that many programs supporting Clustal format cannot read it; fortunately ClustalX can import T-Coffee output so the simplest fix for this issue is usually to import T-Coffee's output into ClustalX and then re-export.

See also

External links

T-Coffee Home Page and Server*[1]
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GNU General Public License
Author: Free Software Foundation
Version: 3
Copyright on the license: Free Software Foundation, Inc.
Publication date: 29 June 2007
OSI approved: Yes
Debian approved: Yes
Free Software:
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A website (alternatively, Web site or web site) is a collection of Web pages, images, videos or other digital assets that is hosted on one or several Web server(s), usually accessible via the Internet, cell phone or a LAN.
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multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In general, the input set of query sequences are assumed to have an evolutionary relationship by which they share a lineage and are descended from a
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Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids. This data, typically obtained by X-ray crystallography or NMR spectroscopy, is submitted by biologists and biochemists from around the world, is released into the public domain,
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Clustal is a widely used multiple sequence alignment computer program. The latest version is 1.83. There are two main variations:
  • ClustalW: command line interface
  • ClustalX: This version has a graphical user interface.

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In bioinformatics, FASTA format is a text-based format for representing either nucleic acid sequences or protein sequences, in which base pairs or protein residues are represented using single-letter codes.
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Clustal is a widely used multiple sequence alignment computer program. The latest version is 1.83. There are two main variations:
  • ClustalW: command line interface
  • ClustalX: This version has a graphical user interface.

..... Click the link for more information.


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