The HMM calibrate tool reads a HMM profile file, scores a large number of synthesized random sequences with it, fits an extreme value distribution (EVD) to the histogram of those scores, and re-saves the hmm file including the EVD parameters.

To avoid modification of the original HMM file you can select a new location for the calibrated profile.

     <img src="/wiki/download/attachments/4227687/Calibrating HMM Model (HMM Calibrate).png"/>