Getting the best out of T-Coffee

  • T-Coffee
    1. Start with the default
    2. Try to combine alternative methods described in the section What Are The Methods Already Integrated in T-Coffee
    3. It can be interesting to combine two alternative matrices like Blosum and Pam
    4. Cheat! and use the reference alignment as an extra library!
    5. Consider that each sequence is named according to the structure it is homologous to. Split the sequences, align each group and align the profiles
    6. Cheat again! This time with the two profiles.
  • Questions should be sent to C.Notredame