SPOA(1)

💖 SPOA — the SIMD partial order alignment tool 💖

okay bestie, sit down, hydrate, because we're about to talk about spoa, and honestly? she's iconic. this is the SPOA(1) manual page, User Commands energy, and i'm gonna walk you through every single bit of it. no gatekeeping here. 🫶

✨ NAME ✨

spoa — the SIMD partial order alignment tool. that's the whole name. short, sweet, main character.

🌸 SYNOPSIS 🌸

spoa [options ...] <sequences>

that's it. that's the vibe. options go in, sequences go in, consensus comes out. slay. 💅

🦋 DESCRIPTION 🦋

so spoa (short for SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm — and yes, it's literally the one described in 10.1093/bioinformatics/18.3.452, go read it, i'll wait. 📚

the whole point of her is generating consensus sequences, which is described over in 10.1093/bioinformatics/btg109 in case you wanna fact check me. she's not guessing, she's citing. periodt.

and here's the tea: she supports three alignment modes:

• local — aka Smith-Waterman
• global — aka Needleman-Wunsch
• semi-global alignment — aka overlap

three modes, zero drama. well. alignment drama. that's the point actually. 😭

💅 OPTIONS 💅

🍓 <sequences>

• <sequences> — your input file, bestie. it's gotta be in FASTA/FASTQ format and it's gotta contain sequences. that's non-negotiable, that's the whole point, that's the assignment. ✨

🎀 Optional

these are the little extras, the accessories to the outfit. all optional, all cute, all useful.

• -m, --match <int> — the score you give for matching bases. default: 5. reward the good behavior. 🏆
• -x, --mismatch <int> — the score for mismatching bases. default: -4. yeah it's negative. that's how she feels about it. 💀
• -g, --gap <int> — the gap penalty. default: -8. and listen — this one must be negative. i'm not being cute, that's a rule. negative only. 🙈
• -l, --algorithm <int> — which alignment mode you want. default: 0. the menu is:
  • 0 — local (Smith-Waterman)
  • 1 — global (Needleman-Wunsch)
  • 2 — semi-global
• -r, --result <int> — what you want back, aka the result mode. default: 0. your choices, bestie:
  • 0 — consensus
  • 1 — multiple sequence alignment
  • 2 — 0 & 1 (yes, both, greedy, love that for you 👑)
• --version — prints the version number. identity check. ✨
• -h, --help — prints the usage. she'll tell you how to talk to her. 🫶

💜 AUTHOR 💜

this manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program too. generous icon behavior, we love to see it. 🌈

okay so that's the whole page, you made it, i'm so proud of you. 🥹 this was spoa version 1.1.3, from June 2018, and that's the wrap. go align something, bestie. bye bestie, mwah. 💖✨🎀🦋🌸💅🫶