nagaraju ngaraju wrote: > I want to do project in homology modelling using modeller but I am > unable to crete .pir file > Can you suggest me in this regard

The alignment file is just a plain text file in a certain format. This format is described at http://salilab.org/modeller/9v5/manual/node440.html

There are also plenty of examples of suitable alignment files in the Modeller distribution (examples directory) and the online tutorial.

Ben Webb, Modeller Caretaker