MAF2ANCHORS(1)

💖 MAF2ANCHORS 💖

okay so bestie, welcome to maf2anchors — she's a lil Perl script from the User Contributed Perl Documentation corner of the world, and her whole job? Turning maf files into Murasaki anchor sets. That's it. That's the gig. And she EATS. 🦋

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✨ NAME ✨

maf2anchors — literally just converts maf files into Murasaki anchor sets, no cap.

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🌸 SYNOPSIS 🌸

maf2anchors <file.maf>

that's it, that's the whole vibe check 🎀

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👑 OPTIONS 👑

• --prefix=<S> — use <S> as a prefix for the output file names. if you don't say anything, she just uses <file.maf> as the prefix instead. lowkey convenient 💅
• --rifts=<I> — allow up to <I> rifts. that's the number, bestie, you pick it. ✨
• --fakeseqs — generate fake sequence length files and sequence stubs, based on the sequence length data that's sitting in the MAF file. fake it till you make it fr fr 🙈
• --trust — trust the comment annotation that TBA added on the second line of the file (if it's even there 👀), which says it lists the tree used in the alignment and all of the sequences involved. this one is defaults to on, queen behavior. if you wanna distrust those TBA tags, use --notrust instead. and ngl, the tea here is that technically this data isn't part of the file format specification at all — it's just crammed into comments that TBA produces 😭 so it might not be present, or might not even be accurate, on all MAF files. that's literally why she gives you the option to distrust it at all. iconic of her honestly 🫶
• --sort — sort the sequences found by --trust, so the result matches the output you would've gotten with --notrust. same energy, different path 🌈

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heads up bestie: that --trust thing is on by default, but the annotation it trusts lives in comments that aren't officially part of the MAF file format. so it might be missing. it might be wrong. choose wisely 💀

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and that's the whole page!! this one's perl v5.40.1, dated 2026-08-12 — mwah, love you, bye 💖✨🎀