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[modeller_usage] Alignment of the sequences



Hi,
I am new to modeller. 
Before building a model, we have to first modify the sequence present in the PIR file. PDB file and PIR file may have few different sequences. So is there any way or software which can align both the sequences (from PDB file and PIR file) so that the sequence present in PIR can be modified. 

Thank you,
Piyush Diyora