---
name: "gt-orffinder"
section: "1"
platform: "linux"
package: "genometools"
version: "1.6.5+ds-2.2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gt-orffinder"
---

# gt-orffinder(1)

Identifies ORFs (open reading frames) in sequences.

## NAME

gt-orffinder - Identifies ORFs (open reading frames) in sequences.

## SYNOPSIS

**gt orffinder** \[option ...\] \[indexname\] \[GFF3\_file ...\]

## DESCRIPTION

- **-types**

  Specify regions which should be searched for open reading frames, e.g. *LTR\_retrotransposon*

- **-allorfs** \[*yes\|no*\]

  search for all ORFs instead of only the longest (default: no)

- **-min** \[*value*\]

  minimum length of ORF (default: 30)

- **-max** \[*value*\]

  maximum length of ORF (default: 10000)

- **-v** \[*yes\|no*\]

  be verbose (default: no)

- **-o** \[*filename*\]

  redirect output to specified file (default: undefined)

- **-gzip** \[*yes\|no*\]

  write gzip compressed output file (default: no)

- **-bzip2** \[*yes\|no*\]

  write bzip2 compressed output file (default: no)

- **-force** \[*yes\|no*\]

  force writing to output file (default: no)

- **-seqfile** \[*filename*\]

  set the sequence file from which to take the sequences (default: undefined)

- **-encseq** \[*filename*\]

  set the encoded sequence indexname from which to take the sequences (default: undefined)

- **-seqfiles**

  set the sequence files from which to extract the features use *--* to terminate the list of sequence files

- **-matchdesc** \[*yes\|no*\]

  search the sequence descriptions from the input files for the desired sequence IDs (in GFF3), reporting the first match (default: no)

- **-matchdescstart** \[*yes\|no*\]

  exactly match the sequence descriptions from the input files for the desired sequence IDs (in GFF3) from the beginning to the first whitespace (default: no)

- **-usedesc** \[*yes\|no*\]

  use sequence descriptions to map the sequence IDs (in GFF3) to actual sequence entries. If a description contains a sequence range (e.g., III:1000001..2000000), the first part is used as sequence ID (*III*) and the first range position as offset (*1000001*) (default: no)

- **-regionmapping** \[*string*\]

  set file containing sequence-region to sequence file mapping (default: undefined)

- **-help**

  display help and exit

- **-version**

  display version information and exit

## REPORTING BUGS

Report bugs to https://github.com/genometools/genometools/issues.