| Developer(s) | Cédric Notredame, Centro de Regulacio Genomica (CRG) - Barcelona |
|---|---|
| Stable release | 9.01 / 13 October 2011 |
| Preview release | 9.01.r1158 |
| Operating system | UNIX, Linux, MS-Windows |
| Type | Bioinformatics tool |
| Licence | GPL |
| Website | www.tcoffee.org |
T-Coffee (Tree-based Consistency Objective Function For alignment Evaluation) is a multiple sequence alignment software using a progressive approach.[1] 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 for 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 most common input formats are supported (FASTA, PIR).
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While the default output is a Clustal-like format, it 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. Another possibility is to request the strict Clustalw output format with the option "-output=clustalw_aln".
An important specificity of T-Coffee is its ability to combine different methods and different data types. In its latest version, T-Coffee can be used to combine protein sequences and structures, RNA sequences and structures. It can also run and combine the output of the most common sequence and structure alignment packages. For a complete list see: tclinkdb.txt
T-Coffee comes along with a sophisticated sequence reformatting utility named seq_reformat. An extensive documentation is available from t_coffee_technical.htm along with a tutorial t_coffee_tutorial.htm
M-Coffee is a special mode of T-Coffee that makes it possible to combine the output of the most common multiple sequence alignment packages (Muscle, ClustalW, Mafft, ProbCons, etc.). The resulting alignments are slightly better than the individual one, but most important the program indicates the alignment regions where the various packages agree upon. Regions of high agreement are usually well aligned.
These are special modes of T-Coffee making it possible to combine sequence and structures in an alignment. The structure based alignments can be carried out using the most common structural aligners such as TMalign, Mustang, and sap.
R-Coffee is a special mode of T-Coffee making it possible to align RNA sequences while using secondary structure information.