---
name: "snap-hmm"
section: "1"
platform: "linux"
package: "snap"
version: "2013-11-29-11"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/snap-hmm"
---

# snap-hmm(1)

Semi-HMM-based Nucleic Acid Parser

## NAME

snap-hmm - Semi-HMM-based Nucleic Acid Parser

## SYNOPSIS

**snap-hmm** \[*options*\] \<**HMM file**\> \<**FASTA file**\> \[*options*\]

## OPTIONS

- **-help**

  report useful information

- **-lcmask**

  treat lowercase as N

- **-plus**

  predict on plus strand only

- **-minus**

  predict on minus strand only

- **-gff**

  output annotation as GFF

- **-ace**

  output annotation as ACED

- **-quiet**

  do not send progress to STDERR

- **-aa** \<file\>

  create FASTA file of proteins

- **-tx** \<file\>

  create FASTA file of transcripts

- **-xdef** \<file\>

  external definitions

- **-name** \<string\>

  name for the gene \[default snap\]