TIMESCOREALN(1)

📦 version 3.3.1, in ubuntu jammy

💖 TIMESCOREALN — like, the whole vibe ✨

okay bestie, welcome to the manual page for timescorealn, part of the User Commands crew 💅 she's giving multiple sequence alignment energy and honestly? iconic.

🌸 NAME 🌸

timescorealn — Global and progressive multiple sequence alignment 🧬✨ no cap, that's the whole thing.

🦋 SYNOPSIS 🦋

timescorealn-avx2 [-options]   -test <test sequences> -ref <reference
alignment> -program <kalign|clustalo|muscle> -o <outfile>

like, that's the shape of it. copy it, don't freestyle it 🙈

💀 DESCRIPTION 💀

so here's the thing, bestie — run it wrong and she will SCREAM at you. first up, this absolute jumpscare:

[2020-08-04 21:41:11] :   ERROR : No test file

and she's like pointing directly at the source, which is:

(time_and_score_aln.c line 111)
⚠️ NOTE: the program appends results to the output file. it does not overwrite. so if you rerun it expecting a fresh file, that's on you, not her. periodt.

🎀 OPTIONS 🎀

  • --scratch — : Scratch directory. [NA] 🗂️ literally the scratch directory spot, default is [NA].

and then she hits you with the usage reminder, bc she cares:

Usage: timescorealn-avx2 [-options]   -test <test sequences> -ref
<reference alignment> -program <kalign|clustalo|muscle> -o <outfile>
⚠️ NOTE: the program appends results to the output file. (yes again. she's serious about it.)
  • --scratch — : Scratch directory. [NA] 🗂️ yep, same one. she said it twice bc she meant it.

and then, when things go sideways, you get this little masterpiece:

[2020-08-04 21:41:11] : WARNING : Something went wrong. Use this program
like this:

with the receipts at:

(time_and_score_aln.c line 154)

followed by, you guessed it, the usage again:

Usage: timescorealn-avx2 [-options]   -test <test sequences> -ref
<reference alignment> -program <kalign|clustalo|muscle> -o <outfile>
⚠️ NOTE: the program appends results to the output file. (third time. the way that she will make sure you know 😭)
  • --scratch — : Scratch directory. [NA] 🗂️ and once more for the people in the back. she's consistent, she's committed, she's serving 💅

👑 AUTHOR 👑

this manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program. 🫶 giving credit where it's due, as she should.

timescorealn 3.2.3 🌈 August 2020 — and that's the whole page, bestie. go slay some alignments 💖✨🌸🦋💅

📦 where this page comes from