From the website:

  T-Coffee is a multiple sequence alignment package. Given a set of sequences
  (Proteins or DNA), T-Coffee generates a multiple sequence alignment.

  Related publications:
  - 3DCoffee: Combining Protein Sequences and Structures within Multiple
    Sequence Alignments.
    O. O'Sullivan, K Suhre, C. Abergel, D.G. Higgins, C. Notredame.
    Journal of Molecular Biology, Vol 340, pp385-395, 2004
  - T-Coffee: A novel method for multiple sequence alignments.  C.Notredame,
    D. Higgins, J. Heringa, Journal of Molecular Biology,Vol 302,
    pp205-217,2000
  - COFFEE: A New Objective Function For Multiple Sequence Alignmnent.
    C.  Notredame, L. Holme and D.G. Higgins,Bioinformatics,Vol 14 (5)
    407-422,1998

Author: Cedric Notredame <cedric.notredame@europe.com>
WWW: http://www.tcoffee.org/