clustalo(1)

💖 clustalo — the manual, bestie edition 💖

okay so you're here for clustalo(1), the USER COMMANDS girlie herself. sit down, grab a lil snack, we're doing multiple sequence alignment and we're doing it cutely. ✨

---

🌸 NAME 🌸

clustalo — a general purpose multiple sequence alignment program for proteins. that's it, that's the whole vibe. 🧬👑

---

✨ SYNOPSIS ✨

clustalo [-h]

one flag. one. she's low maintenance like that. 💅

---

🦋 DESCRIPTION 🦋

Clustal-Omega is a general purpose multiple sequence alignment (MSA) program for proteins. she produces high quality MSAs and is literally capable of handling data-sets of hundreds of thousands of sequences in reasonable time. not me being iconic and scalable at the same time 😭🔥

In default mode, users give a file of sequences to be aligned, and these get clustered to produce a guide tree, and that tree is used to guide a "progressive alignment" of the sequences. no cap, that's the whole pipeline.

There are also facilities for:

• aligning existing alignments to each other 🫶
• aligning a sequence to an alignment 💫
• using a hidden Markov model (HMM) to help guide an alignment of new sequences that are homologous to the sequences used to make the HMM 👑

That last procedure is referred to as "external profile alignment" or EPA. iykyk.

Clustal-Omega uses HMMs for the alignment engine, based on the HHalign package from Johannes Soeding [1]. Guide trees are made using an enhanced version of mBed [2] which can cluster very large numbers of sequences in O(N*log(N)) time. the way that's efficient?? obsessed. Multiple alignment then proceeds by aligning larger and larger alignments using HHalign, following the clustering given by the guide tree. 🌈

⚠️ okay real talk bestie: in its current form Clustal-Omega can only align protein sequences, not DNA/RNA sequences. DNA/RNA is envisioned to become available in a future version, so like… manifesting it. 🙈

---

🎀 USAGE 🎀

Tool usage is available in:

/usr/share/doc/clustalo/README

go read her. she's got the tea. 📖💖

---

💜 DEVELOPMENT 💜

Headers and libraries are available in the libclustalo-dev package. devs, this one's for you. 🛠️✨

---

⭐ CITING ⭐

if you use this in your paper, cite her, periodt:

Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H,
 Remmert M, Söding J, Thompson JD, Higgins DG (2011).  Fast, scalable
generation of high-quality protein multiple sequence alignments
 using Clustal Omega. Mol Syst Biol 7.

academic girlies stay winning 📚👑

---

👑 AUTHOR 👑

• Olivier Sallou (olivier.sallou (at) irisa.fr) — Man page and packaging 🎁
• Conway Institute UCD Dublin (clustalw (at) ucd.ie) — clustalo 🧬

---

and that's the whole page, bestie!! this was version 1.0.3, dated December 14, 2011 — a classic, an icon, a legend. align your proteins and slay 💅💖✨🦋🌸