---
name: "hmm2emit"
section: "1"
platform: "linux"
package: "hmmer2"
version: "2.3.2+dfsg-12+b2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/hmm2emit"
---

# hmm2emit(1)

## NAME

- hmm2emit - generate sequences from a profile HMM

  ## SYNOPSIS

**hmm2emit** *\[options\]* *hmmfile*

## DESCRIPTION

**hmm2emit** reads an HMM file from *hmmfile* containing one or more HMMs, and generates a number of sequences from each HMM; or, if the **-c** option is selected, generate a single majority-rule consensus. This can be useful for various applications in which one needs a simulation of sequences consistent with a sequence family consensus.

By default, **hmm2emit** generates 10 sequences and outputs them in FASTA (unaligned) format.

## OPTIONS

- **-a**

  Write the generated sequences in an aligned format (SELEX) rather than FASTA.

- **-c**

  Predict a single majority-rule consensus sequence instead of sampling sequences from the HMM's probability distribution.  Highly conserved residues (p \>= 0.9 for DNA, p \>= 0.5 for protein) are shown in upper case; others are shown in lower case.  Some insert states may become part of the majority rule consensus, because they are used in \>= 50% of generated sequences; when this happens, insert-generated residues are simply shown as "x".

- **-h**

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

- **-n** *\<n\>*

  Generate *\<n\>* sequences. Default is 10.

- **-o** *\<f\>*

  Save the synthetic sequences to file *\<f\>* rather than writing them to stdout.

- **-q**

  Quiet; suppress all output except for the sequences themselves. Useful for piping or directing the output.

## EXPERT OPTIONS

- **--seed** *\<n\>*

  Set the random seed to *\<n\>,* where  *\<n\>* is a positive integer. The default is to use  **time()** to generate a different seed for each run, which means that two different runs of **hmm2emit** on the same HMM will give slightly different results.  You can use this option to generate reproducible results.

## 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/
```