ALLVERSUSALL(1e)

💖 ALLVERSUSALL(1e) 💖

okay bestie, so this is a page from the EMBOSS Manual for Debian, and it's literally all about allversusall. yes the name is a whole mouthful, we love that for it. grab a boba, we're doing sequence comparison math 🌸

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✨ NAME ✨

allversusall — Sequence similarity data from all-versus-all comparison. that's it, that's the vibe 💅

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✨ SYNOPSIS ✨

allversusall -seqinpath dirlist [-matrix matrixf] [-gapopen float]
             [-gapextend float] -datoutdir outdir -logfile outfile

allversusall -help

no cap, the square brackets mean optional and the rest is mandatory. the way that -seqinpath, -datoutdir and -logfile are just... required. periodt.

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✨ DESCRIPTION ✨

so allversusall is a command line program from EMBOSS (which stands for “the European Molecular Biology Open Software Suite” — iconic name, we stan) 💖

it's part of the "Utils:Database creation" command group(s). it's giving database-builder energy, lowkey 🦋

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✨ OPTIONS ✨

🌸 Input section 🌸

• -seqinpath dirlist — where your sequences live, bestie. Default value: ./
• -matrix matrixf — This option specifies the residue substitution matrix that is used for sequence comparison. Default value: EBLOSUM62

🎀 Required section 🎀

not me leaving this section absolutely empty 😭 it's literally just here, existing, being a required section with nothing in it. we respect its privacy though 🙈

🦋 Additional section 🦋

• -gapopen float — This option specifies the gap insertion penalty. The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. Default value: 10
• -gapextend float — This option specifies the gap extension penalty. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. Default value: 0.5

💜 Output section 💜

• -datoutdir outdir — This option specifies the location of sequence similarity data files (output). Default value: ./
• -logfile outfile — This option specifies the name of ALLVERSUSALL log file (output). The log file contains messages about any errors arising while ALLVERSUSALL ran. Default value: allversusall.log

also there's -help up in the synopsis, in case you need the program to explain itself to you. no shame, we've all been there 🫶

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✨ BUGS ✨

found a bug? 😭 Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031). do it, they wanna hear from you, fr fr 🐛

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✨ SEE ALSO ✨

allversusall is fully documented via the tfm(1) system. iykyk 💫

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✨ AUTHOR ✨

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

• Wrote the script used to autogenerate this manual page. kings of automation, honestly 👑

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✨ COPYRIGHT ✨

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. slay, open source rights 💖

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so that's the whole page, bestie! go forth and compare every sequence against every other sequence, you absolute main character 🌈⭐

this was DOMALIGN 0.1.0+20100721, dated 08/11/2010, and it's been a moment ever since — but the knowledge? timeless. mwah 💋