# hmmer

## Summary

+ **Module Name:** hmmer
+ **Support Level:** Secondary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [http://hmmer.janelia.org/](http://hmmer.janelia.org/)

## Software Description

HMMER is an implementation of profile hidden Markov model (HMM) methods
for sensitive database searches using multiple sequence alignments as
queries. HMMER takes a multiple sequence alignment as input. It can then
build a statistical model called a \"hidden Markov model\" which can be
used as a query into a sequence database to find (and/or align)
additional homologues of the sequence family.
## General Linux

To run this software interactively in a Linux environment run the commands:

	module load hmmer
	hmmbuild [-options] hmmout.file align.file

This will build a profile HMM (hmmout.file) from an input alignment file (align.file).
For a complete list of options, use the -h option, e.g.,

	hmmbuild -h

Other programs available in HMMER are:

- **phmmer** - Search a sequence against a sequence database.
- **jackhmmer** - Iteratively search a sequence against a sequence database.
- **hmmbuild** - Build a profile HMM from an input multiple alignment.
- **hmmsearch** - Search a profile HMM against a sequence database.
- **hmmscan** - Search a sequence against a profile HMM database.
- **hmmalign** - Make a multiple alignment of many sequences to a common profile HMM.
- **hmmconvert** - Convert profile formats to/from HMMER3 format.
- **hmmemit** - Generate sequences from a profile HMM.
- **hmmfetch** - Get a profile HMM by name or accession from an HMM database.
- **hmmpress** - Format an HMM database into a binary format for hmmscan.
- **hmmstat** - Show summary statistics for each profile in an HMM database.

For instructions on how to use each of these, use the `-h` option in the command line or visit the HMMER homepage.