merge k multiple sequence alignments using tcoffee -profile

[Paul Zaharias]

Hi,

I'm currently trying to merge 3 or more alignments using the command :

t_coffee -profile alignment1.fasta  alignment2.fasta  alignment3.fasta -output fasta -outfile tcoffee-result.fasta

...but I'm not really satisfied by the resulting alignment - compare to mafftmerge results for example (but mafftmerge is much slower).

Is there a better way of merging 3 or more alignments using tcoffee?

Many thanks

Paul