---
name: "hmm2convert"
section: "1"
platform: "linux"
package: "hmmer2"
version: "2.3.2+dfsg-12+b2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/hmm2convert"
---

# hmm2convert(1)

## NAME

- hmm2convert - convert between profile HMM file formats

  ## SYNOPSIS

**hmm2convert** *\[options\]* *oldhmmfile* *newhmmfile*

## DESCRIPTION

**hmm2convert** reads an HMM file from *oldhmmfile* in any HMMER format, and writes it to a new file *newhmmfile* in a new format. *oldhmmfile* and  *newhmmfile* must be different files; you can't reliably overwrite  the old file. By default, the new HMM file is written in HMMER 2 ASCII format.

Available formats are HMMER 2 ASCII (default), HMMER 2 binary *(-b)* GCG profile  *(-p)* , and Compugen XSW extended profile  *(-P).*

## OPTIONS

- **-a**

  Convert to HMMER 2 ASCII file. This is the default, so this option is unnecessary.

- **-b**

  Convert to HMMER 2 binary file.

- **-h**

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

- **-p**

  Convert to GCG profile .prf format.

- **-A**

  Append mode; append to *newhmmfile* rather than creating a new file.

- **-F**

  Force; if  *newhmmfile* already exists, and *-A* is not being used to append to the file, hmm2convert will refuse to clobber the existing file unless  *-F* is used.

- **-P**

  Convert the HMM to Compugen XSW extended profile format, which is similar to GCG profile format but has two extra columns for delete-open and delete-extend costs. (I do not believe that Compugen publicly supports this format; it may be undocumented.)

## SEE ALSO

Master man page, with full list of and guide to the individual man pages: see  **[hmmer2(1)](/hmmer2/1.md).**

For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page, http://hmmer.janelia.org/.

## 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/
```