INFOALIGN(1e)

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

💖 INFOALIGN(1e) — bestie, let's read your alignment's whole vibe 💖

okay so this is infoalign, from the <purple>1e</purple> manual section, and it's giving "tell me everything about my multiple sequence alignment" energy. Sit down, grab a lil drink, we're doing this together. 🫶

✨ NAME ✨

infoalign — displays basic information about a multiple sequence alignment. that's it, that's the whole job, and she does it flawlessly 💅

🌸 SYNOPSIS 🌸

infoalign -sequence seqset [-matrix matrix] [-refseq string]
          -plurality float -identity float -outfile outfile
          [-html boolean] -only boolean -heading boolean -usa boolean
          -name boolean -seqlength boolean -alignlength boolean
          -gaps boolean -gapcount boolean -idcount boolean
          -simcount boolean -diffcount boolean -change boolean
          -weight boolean -description boolean

infoalign -help

🦋 DESCRIPTION 🦋

infoalign is a command line program from EMBOSS — and if you don't know, EMBOSS is "the European Molecular Biology Open Software Suite", which is lowkey iconic in the bioinformatics world, no cap. 🧬✨

She belongs to the "Alignment:Multiple,Data retrieval:Sequence data" command group(s). so like, both groups. she's versatile. she contains multitudes. 👑

💅 OPTIONS 💅

🌸 Input section 🌸

  • -sequence seqset — the sequence alignment you want displayed. this is your star of the show, bestie, feed her the alignment. 💖
  • -matrix matrix — the scoring matrix file used when comparing sequences. by default it's EBLOSUM62 (for proteins) or EDNAFULL (for nucleic sequences). both of those live in the data directory of your EMBOSS installation. so like, she already has a go-to fit, but you can swap it out. 🎀
  • -refseq string — give her either the number in the alignment or the name of a sequence, and she'll take that as the reference sequence. the reference sequence is the one every other sequence gets compared against. if you set this to 0, then the consensus sequence is used as the reference sequence instead. and by default? the consensus sequence is the reference. so 0 is basically "yeah do the default thing but, like, on purpose". ✨

🦋 Advanced section 🦋

  • -plurality float — sets a cut-off for the % of positive scoring matches below which there is no consensus. the default plurality is taken as 50% of the total weight of all the sequences in the alignment. Default value: 50.0 🌈
  • -identity float — this lets you set the required number of identities at a position for it to give a consensus. so if you set this to 100%, only columns of identities contribute to the consensus. strict queen behaviour, honestly. Default value: 0.0 ⭐

🍓 Output section 🍓

  • -outfile outfile — put a filename here and the program writes the sequence details into that file. Default value: N 💜
  • -html boolean — Default value: N
  • -only boolean — this is the short-command-line hack for when you only want a couple of things displayed. instead of typing out '-nohead -nousa -noname -noalign -nogaps -nogapcount -nosimcount -noidcount -nodiffcount -noweight' just to get only the sequence length output, you can simply say '-only -seqlength'. she really said "let me save you keystrokes, bestie". 😭💖 Default value: N
  • -heading boolean — Default value: @(!$(only))
  • -usa boolean — Default value: @(!$(only))
  • -name boolean — Default value: @(!$(only))
  • -seqlength boolean — Default value: @(!$(only))
  • -alignlength boolean — Default value: @(!$(only))
  • -gaps boolean — Default value: @(!$(only))
  • -gapcount boolean — Default value: @(!$(only))
  • -idcount boolean — Default value: @(!$(only))
  • -simcount boolean — Default value: @(!$(only))
  • -diffcount boolean — Default value: @(!$(only))
  • -change boolean — Default value: @(!$(only))
  • -weight boolean — Default value: @(!$(only))
  • -description boolean — Default value: @(!$(only))
ok so notice how every single one of those boolean defaults is literally @(!$(only))? yeah. that's the whole bit — they're all on unless you said -only, in which case you opt into each one yourself. iconic design honestly. 💅

💀 BUGS 💀

found a bug? spill it, but like, to the right people:

they will handle it, fr fr. 🫶

🔥 SEE ALSO 🔥

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

👑 AUTHOR 👑

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

  • they wrote the script used to autogenerate this manual page. so the whole page is, like, robot-crafted with love. 🎀

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. so redistribute away, just keep it respectful. 💜

and that's the whole page, bestie!! this was EMBOSS 6.4.0, dated 05/11/2012 — yes she's an elder but she still ate and left no crumbs. go read an alignment, you deserve it. mwah 💅💖✨

📦 where this page comes from