---
name: "hmmcalibrate"
section: "1"
platform: "linux"
package: "hmmer"
version: "2.3.2-5"
release: "Debian 6.0 (Squeeze)"
platforms: ["linux"]
url: "https://new.carta.tech/hmmcalibrate"
---

# hmmcalibrate(1)

## NAME

- hmmcalibrate - calibrate HMM search statistics

  ## SYNOPSIS

**hmmcalibrate** *\[options\]* *hmmfile*

## DESCRIPTION

**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.

## OPTIONS

- **-h**

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

## EXPERT OPTIONS

- **--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).

- **--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.

- **--histfile** *\<f\>*

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

- **--mean** *\<x\>*

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

- **--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.

- **--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.

- **--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.

- **--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.

## SEE ALSO

Master man page, with full list of and guide to the individual man pages: see  **[hmmer(1)](/hmmer/1.md).**

For complete documentation, see the user guide that came with the distribution (Userguide.pdf); or see the HMMER web page, http://hmmer.wustl.edu/.

## COPYRIGHT

```
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine.
Freely distributed under the GNU General Public License (GPL).
```

See the file COPYING in your distribution for details on redistribution conditions.

## AUTHOR

```
Sean Eddy
HHMI/Dept. of Genetics
Washington Univ. School of Medicine
4566 Scott Ave.
St Louis, MO 63110 USA
http://www.genetics.wustl.edu/eddy/
```