---
name: "gt-ltrharvest"
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-ltrharvest"
---

# gt-ltrharvest(1)

Predict LTR retrotransposons.

## NAME

gt-ltrharvest - Predict LTR retrotransposons.

## SYNOPSIS

**gt ltrharvest** \[option ...\] -index \<indexname\>

## DESCRIPTION

- **-index** \[*string*\]

  specify the name of the enhanced suffix array index (mandatory) (default: undefined)

**-range** \[*start* *end*\]

specify range in the input sequence(s) in which LTR pairs are searched (default: \[0..0\])

- **-seed** \[*value*\]

  specify minimum seed length for exact repeats (default: 30)

- **-minlenltr** \[*value*\]

  specify minimum length for each LTR (default: 100)

- **-maxlenltr** \[*value*\]

  specify maximum length for each LTR (default: 1000)

- **-mindistltr** \[*value*\]

  specify minimum distance of LTR startpositions (default: 1000)

- **-maxdistltr** \[*value*\]

  specify maximum distance of LTR startpositions (default: 15000)

- **-similar** \[*value*\]

  specify similaritythreshold in range \[1..100%\] (default: 85.000000)

- **-mintsd** \[*value*\]

  specify minimum length for each TSD (default: 4)

- **-maxtsd** \[*value*\]

  specify maximum length for each TSD (default: 20)

- **-motif** \[*string*\]

  specify 2 nucleotides startmotif + 2 nucleotides endmotif: **\***\* (default: undefined)

- **-motifmis** \[*value*\]

  specify maximum number of mismatches in motif \[0,3\] (default: 4)

- **-vic** \[*value*\]

  specify the number of nucleotides (to the left and to the right) that will be searched for TSDs and/or motifs around 5' and 3' boundary of predicted LTR retrotransposons (default: 60)

- **-overlaps** \[*...*\]

  specify no\|best\|all (default: best)

- **-xdrop** \[*value*\]

  specify xdropbelowscore for extension-alignment (default: 5)

- **-mat** \[*value*\]

  specify matchscore for extension-alignment (default: 2)

- **-mis** \[*value*\]

  specify mismatchscore for extension-alignment (default: -2)

- **-ins** \[*value*\]

  specify insertionscore for extension-alignment (default: -3)

- **-del** \[*value*\]

  specify deletionscore for extension-alignment (default: -3)

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

  verbose mode (default: no)

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

  show *old* tabular output instead of GFF3 on stdout (default: yes)

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

  use sequence descriptions instead of sequence numbers in GFF3 output (default: no)

- **-md5** \[*yes\|no*\]

  add MD5 hashes to seqids in GFF3 output (default: no)

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

  additional motif/TSD output (default: no)

- **-out** \[*string*\]

  specify FASTA outputfilename (default: undefined)

- **-outinner** \[*string*\]

  specify FASTA outputfilename for inner regions (default: undefined)

- **-gff3** \[*string*\]

  specify GFF3 outputfilename (default: undefined)

- **-offset** \[*value*\]

  offset added to GFF3 coordinates (default: 0)

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

  scan the index sequentially instead of mapping it into memory entirely (default: yes)

- **-help**

  display help for basic options and exit

- **-help+**

  display help for all options and exit

- **-version**

  display version information and exit

## ADDITIONAL INFORMATION

For detailed information, please refer to the manual of ltrharvest.

## REPORTING BUGS

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