GT-LTRCLUSTERING(1)

📦
version 1.6.6 · 5 versions
, in ubuntu resolute, ubuntu stonking

💖 GT-LTRCLUSTERING(1) — the GenomeTools Manual, but make it cute 💖

okay bestie, sit down, hydrate, and let me tell you about gt-ltrclustering — the lil GenomeTools command that clusters features of LTRs. that's the whole vibe. it groups those LTR features together and honestly? it ate. 🧬✨

✨ SYNOPSIS ✨

gt ltrclustering [option ...] indexname [GFF3_file ...]

so yeah, you call gt ltrclustering, you hand it some [option ...], then an indexname, and optionally a bunch of GFF3_file ... on top. slay. 🎀

🌸 DESCRIPTION 🌸

this is where all the flags live, and bestie there are a lot of them, so let's go one by one. no skipping, we're not doing that here. 💅

  • -psmall [value] — this one says how many percent of the smaller sequence a match has to cover before the two sequences of that match get clustered. default is 0. lowkey generous of it, ngl.
  • -plarge [value] — same idea but for the larger sequence: how many percent of the larger sequence a match needs to cover to cluster the two sequences of the match. default is also 0. periodt.
  • -o [filename] — redirects the output to the file you specify. default is undefined, so if you don't say anything, it just does its own thing. 🦋
  • -gzip [yes|no] — writes the output file gzip compressed. default is no. say yes if you want that compressed glow. ✨
  • -bzip2 [yes|no] — writes the output file bzip2 compressed. default is no. different algorithm, same energy. 🌈
  • -force [yes|no] — forces writing to the output file. default is no. use this when the file's being dramatic about existing. 😭
  • -help — displays help and exits. your little emotional support flag. 🫶
  • -version — displays version information and exits. main character info dump. 👑
heads up bestie: -gzip and -bzip2 are both off by default (no), and -force is off too — so don't come for me when it doesn't overwrite something, mkay? 🙈

💀 REPORTING BUGS 💀

found a bug? not the cute kind? report it to https://github.com/genometools/genometools/issues and the devs will handle it. fr fr. 🐛

and that's the whole page, bestie!! go cluster some LTR features, you absolute icon. 🎀💜

this has been GenomeTools 1.6.6, dated 11/09/2025 — mwah, kisses, see you in the next manpage 💋✨

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