Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments

Abstract

This paper presents Tcoffee@igs, a new server provided to the community by Hewlet Packard computers and the Centre National de la Recherche Scientifique. This server is a web-based tool dedicated to the computation, the evaluation and the combination of multiple sequence alignments. It uses the latest version of the T-Coffee package. Given a set of unaligned sequences, the server returns an evaluated multiple sequence alignment and the associated phylogenetic tree. This server also makes it possible to evaluate the local reliability of an existing alignment and to combine several alternative multiple alignments into a single new one. Tcoffee@igs can be used for aligning protein, RNA or DNA sequences. Datasets of up to 100 sequences (2000 residues long) can be processed. The server and its documentation are available from: http://igs-server.cnrs-mrs.fr/Tcoffee/.

Figure 1

Typical output of a standard T-Coffee computation. The results can be retrieved at the indicated URL for up to 3 days. ph, a pointer to the phylogenetic tree in Newik format; png, a graphic display of this same tree. Command line indicates the exact command line used by T-Coffee to compute the alignment.

Figure 2

Colored output of T-Coffee. The first lines indicate the average CORE index associated with every sequence. In the rest of the alignment, red residues correspond to highly reliable portions of the multiple alignment. The Cons line is a consensus, it indicates the average reliability value for every column.