BPPALNOPTIM(1)

💖 BPPALNOPTIM(1) 💖

okay so bestie, welcome to bppalnoptim — a lil General Commands Manual entry from the LOCAL section, and no cap, she's a whole vibe. sit down, grab a boba, and let's get into it 🧋✨

✨ NAME ✨

bppalnoptim — Sequence alignment optimization according to the number of sequences vs. number of sites trade-off

like. she optimizes your alignment. it's giving balance. it's giving trade-off. it's giving main character energy 👑

🦋 SYNOPSIS 🦋

bppalnoptim [options]

that's it. that's the whole thing. just run her with some [options] and let her cook 🍓

🌈 AVAILABILITY 🌈

All UNIX flavors 💅

every single one. she does not discriminate. she is for everyone, everywhere, on every flavor of UNIX. iconic behavior fr fr.

🎀 DESCRIPTION 🎀

So here's the tea ☕: bppalnoptim samples sequences from an alignment in order to maximize the number of sites with a given minimal coverage.

read that again. she's out here picking and choosing sequences out of your alignment, and the goal is to squeeze out as many sites as possible while still hitting a minimal coverage you specified. it's a whole optimization situation, and she ate 💅✨

🔥 OPTIONS 🔥

bestie, listen — the options list here is NOT the full menu. like, at all. 👀

You should refer to info physamp or to the online manual of physamp for a complete list of available options.

so yes, this page shows you a lil taste, but the real feast is over at physamp. go look, iykyk 🫶

• --noninteractive=yes — generates output for redirection into a file. like, she'll produce output you can pipe straight into a file instead of being all chatty in your terminal. so good for scripting, ngl 📝
• param=file — reads a file for loading options. basically: hand her a file full of options and she'll load them up. set it and forget it, periodt 💖

💜 AUTHOR 💜

Julien Y. Dutheil.

we stan. thank you for your service 🫡🌸

and that's the whole page, bestie!! it came from the LOCAL section, it's bppalnoptim(1), and honestly? she's a little niche queen and we love her for it 💀👑 stay optimized, drink water, and go read info physamp for the full lore ✨🦋🎀