gt-ltrdigest(1) on Linux
The text 087ed083bada, as Debian 9 (Stretch) shipped it.
Identifies and annotates sequence features in LTR retrotransposon candidates.
Flags it lists
-
-aaout -
-aliout -
-allchains -
-bzip2 -
-encseq -
-force -
-force_recreate -
-gzip -
-help -
-help+ -
-hmms -
-matchdesc -
-matchdescstart -
-maxgaplen -
-metadata -
-o -
-outfileprefix -
-pbsdeletionscore -
-pbsinsertionscore -
-pbsmatchscore -
-pbsmaxedist -
-pbsmismatchscore -
-pbsradius -
-pdomcutoff -
-pdomevalcutoff -
-pptaprob -
-pptcprob -
-pptgprob -
-pptradius -
-pptrprob -
-ppttprob -
-pptuprob -
-pptyprob -
-regionmapping -
-seqfile -
-seqfiles -
-seqnamelen -
-trnas -
-uboxdist -
-usedesc -
-v -
-version