DISTMAT(1e)

📦 version 6.6.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 DISTMAT(1e) 💖

the EMBOSS Manual for Debian, bestie ✨ and yes it's distmat, lowercase, one word, she's iconic like that 💅

🌸 NAME 🌸

distmat — create a distance matrix from a multiple sequence alignment 🧬➡️🔢

✨ SYNOPSIS ✨

distmat -sequence seqset -nucmethod list -protmethod list
        -ambiguous boolean -gapweight float -position integer
        -calculatea boolean -parametera float -outfile outfile

distmat -help

okay so that's the whole vibe right there — every flag you see above is a real thing and you're gonna meet all of them below, one by one, no skipping, we don't do that here 🫶

🦋 DESCRIPTION 🦋

distmat is a command line program from EMBOSS, aka “the European Molecular Biology Open Software Suite” (say that three times fast, I dare you 😭).

She belongs to the "Phylogeny:Molecular sequence" command group(s) — so if you're out here building trees, this is your girl 🌳✨

👑 OPTIONS 👑

🎀 Input section 🎀

  • -sequence seqset — the file that holds your sequence alignment 💖 that's the one you're feeding her.

🍓 Required section 🍓

  • -nucmethod list — multiple substitution correction methods, but for nucleotides 🧬✨
  • -protmethod list — multiple substitution correction methods, but for proteins 🥚💪 same energy, different molecule.
ngl bestie these two are in a section literally called Required, so… yeah. bring them. 👀

🌈 Additional section 🌈

  • -ambiguous boolean — option to use the ambiguous codes in the calculation of the Jukes-Cantor method, or if the sequences are proteins. Default value: N 🙈
  • -gapweight float — option to weight gaps in the uncorrected (nucleotide) and Jukes-Cantor distance methods. Default value: 0. ⚖️
  • -position integer — choose which base positions to analyse in each codon, i.e. 123 (all bases), 12 (the first two bases), 1, 2, or 3 for individual bases. Default value: 123 🔢
  • -calculatea boolean — this will force the calculation of parameter 'a' in the Jin-Nei Gamma distance calculation, otherwise the default is 1.0 (peep the -parametera option below 👇). Default value: N 🧮
  • -parametera float — your user defined parameter 'a', to be used in the Jin-Nei Gamma distance calculation. The suggested value to use is 1.0 (Jin et al.) and this is the default. Default value: 1.0 💫

💜 Output section 💜

  • -outfile outfile — this is where your output goes 🫶 (the original page keeps it short and mysterious, so we're keeping it exactly that way — no cap, that's all she wrote 💀)

💀 BUGS 💀

found a bug? don't suffer in silence bestie, report it 💌

🌟 SEE ALSO 🌟

distmat is fully documented via the tfm(1) system. so if you want the deep lore, that's where it lives 📖✨

🫶 AUTHOR 🫶

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

  • wrote the script used to autogenerate this manual page 🤖💅

This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself. 📜

and that's the whole page, bestie!! 💖✨🎀🦋🌸💅

this one came from EMBOSS 6.4.0, dated 05/11/2012, and it lives in the manual as DISTMAT(1e) — go forth and matrix your distances, you absolute icon 👑🌈⭐

📦 where this page comes from