T-Coffee

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T-Coffee ( Tree -based Consistency Objective Function For alignment Evaluation) is a program in the field of bioinformatics. It is used to create a multiple sequence alignment. The program follows a progressive approach. It generates a collection of pairwise alignments that lead to the multiple sequence alignment. It can also combine pre-computed alignments, and structural information from PDB files using (3D - Coffee). It includes features to improve the quality of alignments to evaluate and some ability for the identification of motifs ( Mocca ). By default alignments are output in aln format ( Clustal ), but it can also various other formats are used, such as PIR, MSF and FASTA. The most common input formats ( FASTA, PIR ) are also supported.

Compared to other alignment programs

Although the default output format ClustalW is similar, there are enough differences to ClustalW / X format, so that many programs that support the Clustal format, it can not use. The original ClustalW format can be output using the option " -output = clustalw_aln ".

An important feature of T-Coffee is the ability to combine different methods and types of data. In the current version, T-Coffee structures and sequences of proteins and RNAs combine. It can also combine structure alignment programs into a single alignment, the output of various commonly used sequence and.

T-Coffee also contains a Reformatierungswerkzeug " seq_reformat ". A detailed documentation is available on the T-Coffee website. Furthermore there is a tutorial.

Variations

M -Coffee

M -Coffee is a special mode of T-Coffee, which allows the output of different multiple sequence alignment packages (Muscle, ClustalW, MAFFT, probcons, etc.) to combine. The resulting alignment is slightly better than the individual. But more importantly, the program marks the regions in the alignment in which match the various individual programs. Regions with a high compliance are generally better snaps.

Expresso and 3D -Coffee

These special modes of T-Coffee allow the joining of sequence and structure in an alignment. The structure-based alignments can with the help of the most commonly used structure alignment programs (eg TMalign, Mustang and sap ) are created.

R -Coffee

R coffee is a special mode of T-Coffee, which makes it possible to alignieren RNA sequences using secondary structure.