HMMER
User's Guide |

**hmmcalibrate** reads an HMM file from *hmmfile,*
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 *hmmfile* now including the EVD parameters.

**hmmcalibrate ** may take
several minutes (or longer) to run. While it is running, a temporary file
called *hmmfile.xxx* is generated in your working directory. If you abort
**hmmcalibrate ** prematurely (ctrl-C, for instance), your original *hmmfile*
will be untouched, and you should delete the *hmmfile.xxx* temporary file.

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**-h**] Print brief help; includes version number and summary of all options, including expert options.

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**-cpu***<n>*] Sets the maximum number of CPUs that the program will run on. The default is to use all CPUs in the machine. Overrides the HMMER_NCPU environment variable. Only affects threaded versions of HMMER (the default on most systems).

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**-fixed***<n>*] Fix the length of the random sequences to*<n>,*where*<n>*is a positive (and reasonably sized) integer. The default is instead to generate sequences with a variety of different lengths, controlled by a Gaussian (normal) distribution.

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**-histfile***<f>*] Save a histogram of the scores and the fitted theoretical curve to file*<f>.*

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**-mean***<x>*] Set the mean length of the synthetic sequences to*<x>,*where*<x>*is a positive real number. The default is 350.

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**-num***<n>*] Set the number of synthetic sequences to*<n>,*where*<n>*is a positive integer. If*<n>*is less than about 1000, the fit to the EVD may fail. Higher numbers of*<n>*will give better determined EVD parameters. The default is 5000; it was empirically chosen as a tradeoff between accuracy and computation time.

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**-pvm**] Run on a Parallel Virtual Machine (PVM). The PVM must already be running. The client program**hmmcalibrate-pvm**must be installed on all the PVM nodes. Optional PVM support must have been compiled into HMMER.

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**-sd***<x>*] Set the standard deviation of the synthetic sequence length distribution to*<x>,*where*<x>*is a positive real number. The default is 350. Note that the Gaussian is left-truncated so that no sequences have lengths <= 0.

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**-seed***<n>*] Set the random seed to*<n>,*where*<n>*is a positive integer. The default is to use**time()**to generate a different seed for each run, which means that two different runs of**hmmcalibrate**on the same HMM will give slightly different results. You can use this option to generate reproducible results for different**hmmcalibrate**runs on the same HMM.

Direct comments and questions to <eddy@genetics.wustl.edu>