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