TANTAN(1)

📦
version 52 · 2 versions
, in ubuntu stonking

✨ TANTAN(1) — User Commands ✨

okay bestie, pull up a chair because we're talking about tantan today 💖 this is its manual page, it lives in section 1 of the Unix manuals (that's the "user commands" girlies club 👑), and it is genuinely so iconic.

🌸 NAME 🌸

tantan — a low complexity and tandem repeat masker for biosequences. yes, for real, that's the whole job. masking. she's a specialist 💅

🦋 SYNOPSIS 🦋

tantan [options] fasta-sequence-file(s)

like, you hand her your FASTA file(s) and some options, and she does her thing ✨

🎀 DESCRIPTION 🎀

Find simple repeats in sequences. that's the assignment, and she ate 🍓

💜 Options (default settings) 💜

ngl these are the knobs you can turn. defaults are in the parentheses so you don't have to guess, no cap 🙈

  • -p — interpret the sequences as proteins
  • -x — letter to use for masking, instead of lowercase
  • -c — preserve uppercase/lowercase in non-masked regions
  • -m — file for letter-pair score matrix
  • -r — probability of a repeat starting per position (0.005)
  • -e — probability of a repeat ending per position (0.05)
  • -w — maximum tandem repeat period to consider (100, but -p selects 50)
  • -d — probability decay per period (0.9)
  • -i — match score (BLOSUM62 if -p, else 2 if -f4, else 1)
  • -j — mismatch cost, 0 means infinite (BLOSUM62 if -p, else 7 if -f4, else 1)
  • -a — gap existence cost (0)
  • -b — gap extension cost, 0 means no gaps (7 if -f4, else 0)
  • -s — minimum repeat probability for masking (0.5)
  • -n — minimum copy number, affects -f4 only (2)
  • -f — output type: 0=masked sequence, 1=repeat probabilities, 2=repeat counts, 3=BED, 4=tandem repeats (0)
  • -h, --help — show help message, then exit
  • --version — show version information, then exit
💡 little vibe note: <pink>-p is lowkey a shape-shifter — she flips your defaults for -w, -i, -j and -b all at once. and <pink>-f4 does her own thing to -i, -j, -b and -n too. slay but keep track of which lane you're in 🫶

🌈 SEE ALSO 🌈

there's no SEE ALSO in this page bb, so instead here's a reminder to read the options twice before piping anything into a loop 😭

and that's the whole page, periodt 👑

this was tantan version 52, and it's dated August 2026 🦋 thank you for coming to my TED talk, go mask some repeats bestie, i'm obsessed with you 💜✨

📦 where this page comes from