How to install ClustalW2 on Ubuntu?

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Installing clustalw2 command-line tool on Ubuntu

Clustal packages [1,2] are quite useful in multiple sequence alignments. Especially, when you need specific outputs from the command-line. In this article, we will install CustalW2 command-line tool on Ubuntu.

Getting started

Open a terminal by pressing Ctrl+Alt+T. Update and upgrade your system using the following commands:

$ sudo apt-get update

$ sudo apt-get upgrade

Installing pre-requisites

Before installing the package, let’s install some pre-requisites.

$ sudo apt-get install -y build-essential

$ sudo apt-get install -y gpp g++ c++ kcc fcc gpp

Downloading ClustalW2

Change to a directory where you wish to download the software. Let’s say, Downloads.

$ cd Downloads/

Download latest version of ClustalW2 from here or use the following command:

$ wget

Installing ClustalW2

Extract the downloaded file.

$ tar xvzf clustalw-2.1.tar.gz

It will create a new directory, namely, ‘clustalw-2.1‘. Change to this directory and install using the following commands:

$ cd clustalw-2.1/

$ ./configure

$ make

$ make install

Now, you can run by typing $ clustalw2 in the terminal.

For a more details on how to use ClustalW2 command-line tool, read this article.


  1. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., … & Higgins, D. G. (2007). Clustal W and Clustal X version 2.0. bioinformatics23(21), 2947-2948.
  2. Sievers, F., & Higgins, D. G. (2014). Clustal Omega, accurate alignment of very large numbers of sequences. In Multiple sequence alignment methods (pp. 105-116). Humana Press, Totowa, NJ.
Tariq is founder of Bioinformatics Review and a professional Software Developer at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

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