The main difference between 3D-Coffee and Expresso is the template specification. While in Expresso the templates are automatically fetched and the template file generated automatically, in 3D-Coffee, they are specified by the user, allowing to a precise selection of the desired templates (including models and homemade structures). 3D-Coffee also allows more flexibility for combining different structural aligners. For instance, the following command line will generate an alignment similar to Expresso:

t_coffee -seq sh3.fasta -method sap_pair -template_file sh3.template_file

When compared with the reference alignment, this alignment, displayed on Figure 5, is the best produced so far, as it manages to correctly align all the structural features displayed in the reference alignment of Figure 1. It is also possible to recapitulate the Expresso mode using the keyword EXPRESSO, while changing the structure comparison methods. For instance, in the following command line, T-Coffee uses BLAST to fetch structural templates and align them with TMalign and SAP:

t_coffee -seq sh3.fasta -method TMalign_pair,sap_pair -template_file EXPRESSO