The original profile HMM is replaced with a new one that contains these EVD parameters. It allows you to access most of hmmcalibrate's parameters from the GCG command line. The program then fits the distribution of these scores to an extreme value distribution, and estimates the EVD parameters mu and lambda for this distribution. These parameters are inserted into the profile HMM file. When using a profile HMM to search a sequence database or using a sequence query to search a profile HMM database, the search is more sensitive if the profile HMM has been calibrated.
Calibration is time-consuming because it is, in a sense, equivalent to a database search in itself.
However, the calibration only has to be performed once, as the extreme value distribution parameters are stored with the profile HMM and will be used whenever you perform profile HMM-sequence database searches. Creating temp file for input to hmmcalibrate. The profile HMM itself wasn't changed but several new lines were added to the file. The line labeled EVD contains the parameters mu and lambda that describe the extreme value distribution of the calibration search. The values on this line are used by HmmerSearch and HmmerPfam.