TRANSFORMSEQ(1)

💖 TRANSFORMSEQ — the transformseq(1) glow-up 💖

okay bestie, listen. this is the manual page for transformseq, section 1 of the manual (so like, the user-commands girly, not some dusty config file). it converts multiple sequence alignments from one format to another, and honestly? it eats. let's get into it 🧚

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✨ NAME ✨

transformseq — convert multiple sequence alignments from one format to another. that's it, that's the whole job, and she does it flawlessly 💅

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🌈 SYNOPSIS 🌈

transformseq [options]  < sequence_data.fa > sequence_logo.eps

like yes, you pipe your alignment in and your converted goodness comes out. the classic stdin → stdout pipeline moment, main character energy fr fr 🫶

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🦋 DESCRIPTION 🦋

so basically, this is a tool for converting multiple sequence alignments from one format to another. that's the vibe. in goes an alignment in one dialect, out comes an alignment in a different dialect. it's giving translator, it's giving multilingual queen 👑

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🎀 OPTIONS 🎀

the flags. the levers. the little knobs that make her do exactly what you want. no cap, there are a lot, and we're covering every single one because we don't do half-finished here 💖

• --version — show the program's version number and then dip (exit). cute, quick, informative.
• -h, --help — show this help message and then exit. your little emergency "wait what do I type" button 🙈

💜 Input/Output Options 💜

the where-does-it-come-from and where-does-it-go section. iconic behavior only ✨

• -f, --fin FILENAME — the sequence input file. if you don't say anything, it reads from stdin (default: stdin), like a mysterious anonymous admirer sliding notes under your door 🍓
• --format-in FORMAT — the multiple sequence alignment format coming in. your options are: clustal, fasta, plain, msf, genbank, nbrf, nexus, phylip, stockholm, intelligenetics, table, array. yes bestie, twelve whole flavors, a whole buffet 🍽️
• -o, --fout FILENAME — the output file. leave it blank and she writes to stdout (default: stdout), just vibing out into your terminal 🌸
• -F, --format-out FORMAT — the multiple sequence alignment format going out. options here: clustal, fasta, plain, intelligenetics, table, array. and the default? fasta. (Default: fasta) — so if you say nothing, fasta it is 💅

🔥 Transformations 🔥

the glow-up section. this is where she actually changes things, and we're obsessed 😭

• --seg — mask low complexity regions in protein sequences. lowkey hiding the boring bits so the interesting parts can shine. slay 💅
• --subsample FRACTION — return a random subsample of the sequences. you give her a FRACTION, she gives you back a random little handful of your sequences. random is random, so don't come for her when it's not the exact ones you wanted 🙈
• --reverse — reverse sequences. flip it, turn it, do a little 180 🔄
• --complement — complement DNA sequences. the A↔T, C↔G situation. DNA but make it opposite 💀

⚠️ heads up bestie: --reverse and --complement are separate flags, so if you're doing the classic reverse-complement on DNA you have to ask for both. no flag is doing double duty here, periodt.

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and that's the whole page, bestie. every flag, every format, every default, preserved like a pressed flower 🌸

this page came from transformseq version 1.0.0, dated January 2026. take care of her and she'll take care of your alignments. mwah, bye 👑💖✨