GT-ORFFINDER(1)

💖 GT-ORFFINDER 💖

okay bestie, welcome to the GenomeTools manual, and specifically to gt-orffinder — she's the one who goes hunting for ORFs (that's open reading frames, keep up 🧬) inside your sequences. manual section 1, she's a command, she's iconic, let's go ✨

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🌸 NAME 🌸

gt-orffinder — Identifies ORFs (open reading frames) in sequences.

like. that's her whole job. that's the gig. 💅

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🎀 SYNOPSIS 🎀

gt orffinder [option ...] [indexname] [GFF3_file ...]

so you call gt with orffinder, then options, then an optional indexname, then zero or more *GFF3_file*s. that's the whole recipe, no cap 🫶

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✨ DESCRIPTION ✨

this is the part where she tells you everything she can do. and she can do a LOT. every single flag, right here, no skips, no "oh you don't need that one" — we're doing all of them 💜

• -types — say which regions should get searched for open reading frames, e.g. LTR_retrotransposon. like, be specific about what you want her looking at 👀
• -allorfs [yes|no] — hunt down all the ORFs instead of just the longest one (default: no). so by default she's picking a favourite, and that favourite is the longest. she's not sorry.
• -min [value] — the minimum length of an ORF (default: 30). anything shorter than this? not invited to the party 🚫
• -max [value] — the maximum length of an ORF (default: 10000). anything longer? also not invited. boundaries, babe.
• -v [yes|no] — be verbose (default: no). turn this on and she will talk. she will tell you things. she will not stop telling you things 😭
• -o [filename] — redirect output to the specified file (default: undefined). so your terminal doesn't eat the whole scrollback, you know?
• -gzip [yes|no] — write a gzip-compressed output file (default: no). zip it, queen 🗜️
• -bzip2 [yes|no] — write a bzip2-compressed output file (default: no). different compression, same energy ✨
• -force [yes|no] — force writing to the output file (default: no). yes she checks first, yes this overrides it, be careful bestie 🙈
• -seqfile [filename] — set the sequence file she takes the sequences from (default: undefined).
• -encseq [filename] — set the encoded sequence indexname she takes the sequences from (default: undefined).
• -seqfiles — set the sequence files she extracts the features from. use -- to terminate the list of sequence files — do not forget the --, fr fr, that's how she knows you're done listing 🛑
• -matchdesc [yes|no] — search the sequence descriptions from the input files for the sequence IDs you want (the ones in the GFF3), and report the first match (default: no).
• -matchdescstart [yes|no] — exactly match the sequence descriptions from the input files for the desired sequence IDs (in GFF3), going from the beginning to the first whitespace (default: no). precision. she's precise.
• -usedesc [yes|no] — use sequence descriptions to map the sequence IDs (in GFF3) onto actual sequence entries. and listen: if a description contains a sequence range (like III:1000001..2000000), the first part gets used as the sequence ID (III) and the first range position as the offset (1000001) (default: no). the way that she just… parses that. obsessed 💅
• -regionmapping [string] — set the file containing the sequence-region-to-sequence-file mapping (default: undefined).
• -help — display help and exit. bestie behaviour honestly 🫶
• -version — display version information and exit.

heads up: -o, -gzip, -bzip2 and -force all default to undefined/no — meaning if you don't say anything, she just prints to your terminal and doesn't touch your files. no surprises. we love a girl with boundaries 💖

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😤 REPORTING BUGS 😤

found a bug? tell the devs, they're nice, they're on GitHub:

https://github.com/genometools/genometools/issues

do NOT just suffer in silence, that's not the vibe, that's not self-care 🌸

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and that's the whole page!! this was GenomeTools 1.6.6, dated 11/09/2025 — so if you're reading this, hi, you're officially caught up, go find some ORFs, slay, periodt 👑💖🧚