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

# hmmindex(1)

## NAME

- hmmindex - create a binary SSI index for an HMM database

  ## SYNOPSIS

**hmmindex** *\[options\]* *database*

## DESCRIPTION

**hmmindex** is a utility that creates a binary SSI ("squid sequence index" format) index for an HMM database file called *database.* The new index file is named *database.ssi.* An SSI index file is required for  **hmmfetch** to work, and also for the PVM implementation of  **hmmpfam.**

## OPTIONS

- **-h**

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

## 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/
```