---
name: "gt-tirvish"
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-tirvish"
---

# gt-tirvish(1)

Identify Terminal Inverted Repeat (TIR) elements,such as DNA transposons.

## NAME

gt-tirvish - Identify Terminal Inverted Repeat (TIR) elements,such as DNA transposons.

## SYNOPSIS

**gt tirvish** \[option ...\] -index INDEXNAME

## DESCRIPTION

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

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

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

  specify minimum seed length for exact repeats (default: 20)

- **-mintirlen** \[*value*\]

  specify minimum length for each TIR (default: 100)

- **-maxtirlen** \[*value*\]

  specify maximum length for each TIR (default: 1000)

- **-mintirdist** \[*value*\]

  specify minimum distance of TIRs (default: 500)

- **-maxtirdist** \[*value*\]

  specify maximum distance of TIRs (default: 10000)

- **-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)

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

  specify xdropbelowscore for extension-alignment (default: 5)

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

  specify TIR similarity threshold in therange \[1..100%\] (default: 85.000000)

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

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

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

  specify minimum length for each TSD (default: 2)

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

  specify maximum length for each TSD (default: 11)

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

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

- **-hmms**

  profile HMM models for domain detection (separate by spaces, finish with --) in HMMER3 format Omit this option to disable pHMM search.

- **-pdomevalcutoff** \[*value*\]

  global E-value cutoff for pHMM search default 1E-6

- **-pdomcutoff** \[*...*\]

  model-specific score cutoff choose from TC (trusted cutoff) \| GA (gathering cutoff) \| NONE (no cutoffs) (default: GA)

- **-maxgaplen** \[*value*\]

  maximal allowed gap size between fragments (in amino acids) when chaining pHMM hits for a protein domain (default: 50)

- **-refseqs** \[*string*\]

  specify the name of the gene sequences to scan for inside candidates (default: undefined)

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

  use sequence descriptions instead of sequence numbers in GFF3 output (default: yes)

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

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

- **-help**

  display help for basic options and exit

- **-help+**

  display help for all options and exit

- **-version**

  display version information and exit

## REPORTING BUGS

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