GT-SEQMUTATE(1)

GT-SEQMUTATE 💅✨

okay bestie, welcome to the GenomeTools Manual page for gt-seqmutate — she mutates the sequences of the given sequence file(s) and honestly? she's giving chaos gremlin in the best way 🦋

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✨ NAME ✨

gt-seqmutate — mutate the sequences of the given sequence file(s), fr fr 🧬

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🎀 SYNOPSIS 🎀

gt seqmutate [option ...] [sequence_file ...]

like that's it, that's the whole vibe check 👑

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💖 DESCRIPTION 💖

okay so first, the options, because we love a structured queen:

• -rate [value] — sets the mutation rate (default: 1) 🌸
• -width [value] — sets the output width for FASTA sequence printing. 0 disables formatting entirely (default: 0) ✨
• -o [filename] — redirects output to the specified file (default: undefined) 💜
• -gzip [yes|no] — write a gzip compressed output file (default: no) 🎀
• -bzip2 [yes|no] — write a bzip2 compressed output file (default: no) 🎀
• -force [yes|no] — force writing to the output file (default: no) 🔥
• -help — display help and exit 🫶
• -version — display version information and exit 🌈

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🧚 how the mutating actually goes down 🧚

so for each and every position in the given sequences, it is randomly determined with probability (mutation rate / 100) whether that given position gets mutated. yes bestie, every single position, no cap 👀

and if it does get picked? then:

• in 80% of the cases a substitution is performed 🔁
• in 10% an insertion is performed ➕
• and in 10% a deletion is performed ➖

for substitution and insertion events, the nucleotide is generated randomly without regard to the original nucleotide. which means — and this is the part that lives in my head rent free — resubstitutions are possible 😭 like she genuinely does not care what was there before, she's just picking.

this whole procedure equals the one described on page 1867 of the following paper 📄:

T.D. Wu and C.K. Watanabe. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics, 21(9):1859-1875, 2005.

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💀 REPORTING BUGS 💀

found a bug? not the vibe. report bugs to https://github.com/genometools/genometools/issues and the maintainers will handle it, periodt 🙈

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and that's the whole page, bestie — GenomeTools 1.6.6, dated 11/09/2025 💖 go forth and mutate responsibly (or don't, I'm a manpage not a cop) ✨🦋💅