This mode has been developed to align large protein families (>500 proteins). Rather than building the standard T-Coffee library, Fast M-Coffee runs a few fast aligners (by default Kalign, MAFFT and MUSCLE) on the entire dataset and combines their output into one single final alignment. The following command will launch Fast M-Coffee:

t_coffee -seq sh3.fasta -mode fmcoffee

M-Coffee the same three output files as T-Coffee:

• sh3.dnd: guide tree used to assemble the progressive alignment.
• sh3.aln: final alignment given in ClustalW format.
• sh3.html: final alignment colored in function of the CORE index from red (very consistent) to blue (poorly consistent) (Figure 3).

The color code in the resulting alignment indicates the agreement within the library and therefore the agreement between the combined methods. The agreement between fast methods is often high, even in regions inaccurately aligned. By contrast, a low consistency provides a better indication of inaccurate alignment. This reflects well the difficulty for most standard aligners to accurately align small protein domains poorly conserved in sequence like the SH3 domains. If needed, the user can also specify a different combination of methods, for instance, using the following command line:
t_coffee –seq sh3.fasta –method=muscle_msa,probcons_msa,clustalw_msa
The list of all available methods installed on the user system can be displayed by running the following command:
t_coffee