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

# hmm-assembler.pl(1)

SNAP module hmm-assembler.pl

## NAME

hmm-assembler.pl - SNAP module hmm-assembler.pl

## SYNOPSIS

**hmm-assembler.pl** \[*-OPTIONS* \[*-MORE\_OPTIONS*\]\] \[*--*\] \[*PROGRAM\_ARG1* ...\]

## OPTIONS

### The following single-character options are accepted:

With arguments: **-i** **-e** **-A** **-D** **-M** **-S** **-C** **-I** **-N** **-a** **-3** **-5** **-Z** **-c**

Boolean (without arguments): **-r** **-o** **-x** **-p** **-t** **-1**

Options may be merged together.  **--** stops processing of options. Space is not required between options and their arguments.

Options:

- **-i**

  \<length\>       \[500\]

- **-e**

  \<length\>       \[1000\]

- **-A**

  \<order:length\> \[0:30\]

- **-D**

  \<order:length\> \[0:9\]

- **-M**

  \<order:length\> \[0:15\]

- **-S**

  \<order:length\> \[0:9\]

- **-C**

  \<order\>        \[4\]

- **-I**

  \<order\>        \[4\]

- **-N**

  \<order\>        \[4\]

- **-3**

  \<order:length\> \[\]  include 3'UTR model, requires **-a**

- **-a**

  \<order:length\> \[\]  include PolyA model, requires **-3**

- **-5**

  \<order:length\> \[\]  include 5'UTR moel, requires **-p**

- **-p**

  include generic promoter model, requires **-5**

- **-r**

  include generic repeat model

- **-o**

  include reverse ORF model

- **-x**

  use explicit duration intron model

- **-t**

  include C.elegans trans-splicing, requires **-p**, **-5**

- **-Z**

  \<clade\>            sets clade-specific values (worm, fly, plant)

- **-1**

  single gene model

- **-c** \<score\>

  include GC-AG splice donor model