---
name: "gt-ltrdigest"
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-ltrdigest"
---

# gt-ltrdigest(1)

Identifies and annotates sequence features in LTR retrotransposon candidates.

## NAME

gt-ltrdigest - Identifies and annotates sequence features in LTR retrotransposon candidates.

## SYNOPSIS

**gt ltrdigest** \[option ...\] gff3\_file

## DESCRIPTION

- **-outfileprefix** \[*string*\]

  prefix for output files (e.g. *foo* will create files called *foo\_\*.csv* and *foo\_\*.fas*) Omit this option for GFF3 output only.

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

  output metadata (run conditions) to separate file (default: yes)

- **-seqnamelen** \[*value*\]

  set maximal length of sequence names in FASTA headers (e.g. for clustalw or similar tools) (default: 20)

**-pptlen** \[*start* *end*\]

required PPT length range (default: \[8..30\])

**-uboxlen** \[*start* *end*\]

required U-box length range (default: \[3..30\])

- **-uboxdist** \[*value*\]

  allowed U-box distance range from PPT (default: 0)

- **-pptradius** \[*value*\]

  radius around beginning of 3' LTR to search for PPT (default: 30)

- **-pptrprob** \[*value*\]

  purine emission probability inside PPT (default: 0.970000)

- **-pptyprob** \[*value*\]

  pyrimidine emission probability inside PPT (default: 0.030000)

- **-pptgprob** \[*value*\]

  background G emission probability outside PPT (default: 0.250000)

- **-pptcprob** \[*value*\]

  background C emission probability outside PPT (default: 0.250000)

- **-pptaprob** \[*value*\]

  background A emission probability outside PPT (default: 0.250000)

- **-ppttprob** \[*value*\]

  background T emission probability outside PPT (default: 0.250000)

- **-pptuprob** \[*value*\]

  U/T emission probability inside U-box (default: 0.910000)

- **-trnas** \[*filename*\]

  tRNA library in multiple FASTA format for PBS detection Omit this option to disable PBS search.

**-pbsalilen** \[*start* *end*\]

required PBS/tRNA alignment length range (default: \[11..30\])

**-pbsoffset** \[*start* *end*\]

allowed PBS offset from LTR boundary range (default: \[0..5\])

**-pbstrnaoffset** \[*start* *end*\]

allowed PBS/tRNA 3' end alignment offset range (default: \[0..5\])

- **-pbsmaxedist** \[*value*\]

  maximal allowed PBS/tRNA alignment unit edit distance (default: 1)

- **-pbsradius** \[*value*\]

  radius around end of 5' LTR to search for PBS (default: 30)

- **-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: NONE)

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

  output pHMM to amino acid sequence alignments (default: no)

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

  output amino acid sequences for protein domain hits (default: no)

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

  output features from all chains and unchained features, labeled with chain numbers (default: no)

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

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

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

  force recreation of hmmpressed profiles (default: no)

- **-pbsmatchscore** \[*value*\]

  match score for PBS/tRNA alignments (default: 5)

- **-pbsmismatchscore** \[*value*\]

  mismatch score for PBS/tRNA alignments (default: -10)

- **-pbsinsertionscore** \[*value*\]

  insertion score for PBS/tRNA alignments (default: -20)

- **-pbsdeletionscore** \[*value*\]

  deletion score for PBS/tRNA alignments (default: -20)

- **-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 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.