EDLIB-ALIGNER(1)

📦 version 1.2.7, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 EDLIB-ALIGNER 💖

okay bestie, welcome to edlib-aligner — it's the edlib sequence alignment tool that does its thing using edit distance ✨ this is section 1 of the manual, so it's a user command, meaning you just run it in your terminal like the main character you are 💅

🌸 NAME 🌸

edlib-aligner — edlib sequence alignment tool using edit distance 🧬✨

🦋 SYNOPSIS 🦋

edlib-aligner [options...] <queries.fasta> <target.fasta>

so basically you give it some queries.fasta and a target.fasta and it goes off 🫶

👑 OPTIONS 👑

  • -s — if you specify this, there is no score or alignment output at all. it's giving silent mode 🤫 (yes, the flag is literally just vibes and no words)
  • -m HW|NW|SHW — the alignment mode it's gonna use. [default: NW] — pick your fighter ⭐
  • -n N — score gets calculated only for the N best sequences, and "best" means the ones with the smallest score, periodt. if N = 0 then all sequences get calculated. ngl, specifying a small N can make the total calculation sooo much faster 🔥 [default: 0]
  • -k K — sequences with a score > K get discarded, sorry bestie 💀 smaller k = faster calculation, that's just math. if it's -1, then no sequences will be discarded at all, everyone's invited 🎀 [default: -1]
  • -p — if you specify this, the alignment path will be found and printed. heads up though: this may significantly slow down the calculation 😭 the price of beauty, fr fr
  • -l — if you specify this, start locations will be found and printed, and each start location corresponds to one end location 🦋 this may somewhat slow down the calculation, but it's still faster than finding the alignment path and it does not consume any extra memory — iconic, honestly 👑
  • -f NICE|CIG_STD|CIG_EXT — the format used to print the alignment path. psst, this can only be used with -p ⚠️ NICE gives you the visually attractive format (aesthetic ✨), CIG_STD gives standard cigar format, and CIG_EXT gives extended cigar format. [default: NICE]

💜 AUTHOR 💜

this manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program 🫶 giving credit where credit is due, as we should 💅

k that's the whole page bestie, go align something and slay 🌈

edlib-aligner 1.2.3 · June 2018 — mwah, see u next manpage 💖🎀

📦 where this page comes from