To get an overview of the Biskit.Mod modules the example script ~biskit/scripts/Mod/modelling_example.py is a good start. The script 
is fairly well documented by the comments within the script itself.

To produce an example of the modeling run the script modelling_example.py from within the directory ~biskit/test/Mod:

modelling_example.py -q project/target.fasta -o project -log -view 

This requires that you have installed 
(according to ~biskit/docs/install_helper_apps.txt):
- NCBI-toolkit (blastall, formatdb, blastclust ..)
- local pdbaa and swissprot database (local pdb database is optional)
- T-Coffee
- clustalW
- SAP
- Modeller

For a more thorough introduction of Biskit.Mod see ~biskit/doc/mod.howto.
