---
name: "hmmpress"
section: "1"
platform: "linux"
package: "hmmer"
version: "3.4+dfsg-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/hmmpress"
---

# hmmpress(1)

prepare a profile database for hmmscan

## NAME

hmmpress - prepare a profile database for hmmscan

## SYNOPSIS

**hmmpress** \[*options*\] *hmmfile*

## DESCRIPTION

Constructs binary compressed datafiles for  **hmmscan**, starting from a profile database *hmmfile* in standard HMMER3 format. The  **hmmpress** step is required for **hmmscan** to work.

Four files are created: *hmmfile***.h3m,** *hmmfile***.h3i,** *hmmfile***.h3f,** and *hmmfile***.h3p.** The  *hmmfile***.h3m** file contains the profile HMMs and their annotation in a binary format. The  *hmmfile***.h3i** file is an SSI index for the *hmmfile***.h3m** file. The *hmmfile***.h3f** file contains precomputed data structures for the fast heuristic filter (the MSV filter). The *hmmfile***.h3p** file contains precomputed data structures for the rest of each profile.

*hmmfile* may not be '-' (dash); running **hmmpress** on a standard input stream rather than a file is not allowed.

## OPTIONS

- **-h**

  Help; print a brief reminder of command line usage and all available options.

- **-f**

  Force; overwrites any previous hmmpress'ed datafiles. The default is to bitch about any existing files and ask you to delete them first.

## SEE ALSO

See  [**hmmer**(1)](/hmmer/1.md) for a master man page with a list of all the individual man pages for programs in the HMMER package.

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

## COPYRIGHT

```
Copyright (C) 2023 Howard Hughes Medical Institute.
Freely distributed under the BSD open source license.
```

For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER web page  (http://hmmer.org/).

## AUTHOR

```
http://eddylab.org
```