GT-MATCHTOOL(1)

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

💖 NAME 💖

gt-matchtool — bestie, this one parses match formats and/or invokes matching tools. That's it. That's the whole job. Slay. ✨

🌸 SYNOPSIS 🌸

gt matchtool [option ...]

🦋 DESCRIPTION 🦋

Okay so listen, this tool is lowkey a whole vibe router — you tell it which match format you're working with (or which external matching tool to fire up), and it handles the rest. Here's every single knob, no cap:

  • -type [...] — pick your match file format. The options are giving variety:
    • OPENMATCH: the open match format, e.g. vmatch
    • BLASTOUT: tabular BLAST output (-m 8)
    • BLASTALLP: invoke BLASTALL with blastp
    • BLASTALLN: invoke BLASTALL with blastn
    • BLASTP: invoke blastp
    • BLASTN: invoke blastn
    • LAST: invoke LAST
    • SW: use Smith-Waterman
    • default: OPENMATCH (yes, that's the starting point, periodt)
  • -matchfile [filename] — set the input file name. Default: undefined (aka it's not set, so you gotta give it one bestie 🙈)
  • -db [filename] — set the database file name. Default: undefined again 💀
  • -swminlen [value] — set the minimum required alignment length (this one's for Smith-Waterman alignment). Default: 10
  • -swmaxedist [value] — set the maximum allowed edit distance (also for Smith-Waterman alignment). Default: 0
  • -query [filename] — set the query file name. Default: undefined, the trio of undefined defaults is iconic honestly 😭
  • -help — display help and exit. Main character move, always valid. 👑
  • -version — display version information and exit. Quick lil flex. ⭐

🎀 REPORTING BUGS 🎀

Found a bug? Not the vibe. Please report it to https://github.com/genometools/genometools/issues and the devs will handle it. 🫶

Okay that's a wrap! This was GenomeTools 1.6.6, dated 11/09/2025 — the GT-MATCHTOOL(1) page from the GenomeTools manual. Go forth and match things, bestie. 💅✨🌈

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