Nucleic Acids Research, 2007, Vol. 35, Web Server issue W647 Figure 1. Method selection on the advanced M-Coﬀee server form. Each check box corresponds to either a pairwise (_pair) or a multiple sequence alignment method (_msa). Users should choose their methods of choice in order to combine them. element is score_html that will cause the server to produce a colored version of the ﬁnal alignment (Figure 2). In this output, residues are individually colored according to the consistency of their alignment with the T-Coﬀee library. Residues in red are in perfect agreement with every constituting multiple alignment while those in blue have the lowest agreement (i.e. the lowest support in the individual MSAs). Previous analysis indicates that 90% of the residues having a score of 7 or higher (dark yellow, orange and red) are correctly aligned (24). A text version of this output is available as score_ascii where each residue is replaced with its consistency estimation on a scale between 0 and 9 (9 corresponding to the red-brick residues in the color-output). These score_ascii ﬁles can be used to process multiple alignments (block extraction) using seq_reformat, one of the utilities distributed along with T-Coﬀee. For this purpose, users can download their alignment, the score_ascii ﬁle and use the Figure 2. Typical colored output. This output was obtained by using the kinase1_ref5 from BaliBase. Correctly aligned residues (as judged from the reference) are in upper case, non-correct ones are in lower case. In this colored output, each residue has a color that indicates the agreement of the individual MSAs with respect to the alignment of that speciﬁc residue. Dark red indicates residues aligned in a similar fashion among all the individual MSAs; blue indicates a very low agreement. Dark yellow, orange and red residues can be considered to be reliably aligned.