Hi Smith,

PHENIX uses muscle (http://www.drive5.com/muscle/) to align sequences (https://www.phenix-online.org/documentation/phenix_gui.html#other-tools).

You can access muscle with "phenix.muscle" on the command line.

Hope this helps,
Folmer Fredslund

2015-04-10 9:20 GMT+02:00 Smith Liu <smith_liu123@163.com>:
Dear All,
 
Will you please tell me the Phenix command to align the PDB sequence and input sequence?
 
I am looking forward to getting your reply.
 
Smith



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Folmer Fredslund