Sehrish Batool wrote: > As the reliability of predicted structure depends on the reliability > of alignment of protein sequences, I want to ask which one tool can > provide the best and most reliable alignment of two protein sequences > that can be used as input in MODELLER?

There are many tools that can be used for sequence alignment. We recommend our align2d or salign methods (see "Alignment of protein structures with sequences" at http://salilab.org/modeller/9v7/manual/node288.html) but in principle you can obtain the input alignment for modeling from any source.

Ben Webb, Modeller Caretaker