T Coffee

Comparisons with other alignment software

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

Variations

M-Coffee 

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 importantly the program indicates the alignment regions where the various packages agree upon. Regions of high agreement are usually well aligned.

Expresso and 3D-Coffee 

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 

a special mode of T-Coffee making it possible to align RNA sequences while using secondary structure information.

PSI-Coffee 

aligns distantly related proteins using homology extension (slow and accurate)

TM-Coffee 

aligns transmembrane proteins using homology extension

Pro-Coffee 

aligns homologous promoter regions

Accurate 

automatically combine the most accurate modes for DNA, RNA and Proteins (experimental!)

Combine 

combines two (or more) multiple sequence alignments into a single one.

Evaluation

TCS 

(Transitive Consistency Score) an extended version of the T-Coffee scoring scheme. It uses T-Coffee libraries of pairwise alignments to evaluate any third party MSA. Pairwise projections can be produced using fast or slow methods, thus allowing a trade-off between speed and accuracy. TCS has been shown to lead to significantly better estimates of structural accuracy and more accurate phylogenetic trees against Heads-or-Tails, GUIDANCE, Gblocks, and trimAl.