---
name: "cm2hmm"
section: "1"
platform: "linux"
package: "infernal"
version: "1.0.2-2"
release: "Debian 7 (Wheezy)"
platforms: ["linux"]
url: "https://new.carta.tech/cm2hmm"
---

# cm2hmm(1)

## NAME

- cm2hmm - build a rigorous HMM-based filter from an existing covariance model (CM)

  ## SYNOPSIS

**cm2hmm** *cmfile* *hmmfile* *background \[background parameters\]* *HMMtype* *optimizer \[optimizer parameters\]*

## DESCRIPTION

**cm2hmm** reads a covariance model (CM) from *cmfile,* constructs a hidden-Markov model (HMM) that preserves some information of the CM and saves the HMM to *hmmfile.* The HMM can be used as a rigorous pre-filtering step to searching with the CM.

The CM file must be in the standard format output used by Infernal.

## OPTIONS

- **--help**

  Print brief help; includes summary of command-line parameters.

- **background** *\[background parameters\]*

  Select the model of background sequence. **uniform** gives all bases equal probability (25%). **gc** *\<fraction\>* specifies the G+C content. *\<fraction\>* should be a number between 0 and 1. **file** *\<filename\>* loads the base distribution from a file in a specific format.

- **HMMtype**

  Specify the type of HMM to be used; options are **compact** and **expanded.** Compact-type models are generally faster, but expanded-type models may provide better filtering.

- **optimizer** *\[optimizer parameters\]*

  Specify which mathematical optimizer is to be used to create  the final model.  Currently the only option is **cfsqp** which takes two paramters: *\<B\> \<C\>.* B=0, C=1 are reasonable choices.  (See the CFSQP manual for further details.)

## SEE ALSO

For complete documentation, see the User's Guide (Userguide.pdf) that came with the distribution; or see the Infernal web page, http://infernal.janelia.org/.

## COPYRIGHT

```
Copyright (C) 2009 HHMI Janelia Farm Research Campus.
Freely distributed under the GNU General Public License (GPLv3).
```

See the file COPYING that came with the source for details on redistribution conditions.

## AUTHOR

```
Eric Nawrocki, Diana Kolbe, and Sean Eddy
HHMI Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147
http://selab.janelia.org/
```