GT-TIRVISH(1)

💖 GT-TIRVISH(1) 💖

okay bestie, welcome to the GenomeTools Manual page for gt-tirvish, and yes we're doing this together, grab a boba 🧋

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✨ NAME ✨

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

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🌸 SYNOPSIS 🌸

gt tirvish [option ...] -index INDEXNAME

like… the -index is not optional, babes. it's giving mandatory. 🫶

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🦋 DESCRIPTION 🦋

here's the whole menu of options, no skips, no skimming, we're reading all of them together ✨

• -index [string] — specify the name of the enhanced suffix array index. this one is mandatory, no cap. (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 the range [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

lowkey the vibes here are immaculate: two undefined defaults, a bunch of numbers you should probably not touch unless you know what you're doing, and -help+ if you want the full lore drop 📚

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💀 REPORTING BUGS 💀

found a bug? not the moment, bestie 😭 report bugs to https://github.com/genometools/genometools/issues. they'll handle it, fr fr 🫶

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and that's a wrap, my love 💜 this was GenomeTools 1.6.6, dated 11/09/2025, and the page is GT-TIRVISH(1). go identify some Terminal Inverted Repeats, you absolute icon 👑✨🎀