You don't necessarily have to go through the hassle to install Clustal on your computer. Instead, you can run Clustal online on several servers on the web:

Download Clustal W/X

Clustal 2 comes in two flavors: the command-line version Clustal W and the graphical version Clustal X. Precompiled executables for Linux, Mac OS X and Windows (incl. XP and Vista) of the most recent version (currently 2.1) along with the source code are available for download here. You can also browse for older versions (Clustal W 1.81, Clustal V etc).
The current version of Clustal 2 is also mirrored on the EBI ftp site .

Clustal 2.1 is released under the GNU Lesser GPL.



Please have a look at Clustal X's builtin help menu or if you are using Clustal W use clustalw[2] -help or /help (depending on your platform and version of Clustal). Online versions (which might be out of date) can be found here: Clustal W and Clustal X. There are a couple of references on how to use Clustal W/X on the net. A very nice tutorial which also covers advanced features like using secondary structures for profile alignment is "Using Clustal X for multiple sequence" by Jarno Tuimala (local mirror).


Contact / Bugs

Clustal is currently maintained at the Conway Institute UCD Dublin by Des Higgins, Fabian Sievers, David Dineen, and Andreas Wilm. You can reach us at

If you want to report a bug please make sure, that you are using the most recent version of Clustal. Please also check if the bug has already been reported on our Bugzilla webpage

Known issues (2.1)

Guide tree creation
Hitting return when creating the guide tree cancels the alignment.
UPGMA guide trees
Under some pathological cases, it is possible to create UPGMA guide trees with non-equidistant tips.
Postscript output
If a Postscript output file contains many sequences, Clustal will shrink the font size in an attempt to fit them all on one page. This may cause the sequences to be unreadable. One workaround is to increase the paper size.
Clustal cannot read files saved on WinXp Desktop (Japanse/Chinese environment)
If this happens copy the files to another location and try to open it again.


We would like to thank all Clustal users who have send in feedback, bug reports and feature requests. Thanks to all people who helped testing and packaging Clustal, in particular Charles Plessy, Richard Christen, Blake Mertz, Ian Jeffery...

SFI logo

Recent work on Clustal was mainly funded by Science Foundation Ireland


2010-11-17  ·  Version 2.1 released. See CHANGELOG

2009-09-23  ·  Version 2.0.12 released. See CHANGELOG

2009-04-16  ·  Version 2.0.11 released. See CHANGELOG

2008-10-14  ·  Version 2.0.10 released. See CHANGELOG

2008-06-23  ·  Version 2.0.9 released. See CHANGELOG

2008-06-03  ·  Version 2.0.8 released. See CHANGELOG

2008-05-13  ·  Version 2.0.7 released. See CHANGELOG

2008-04-24  ·  Version 2.0.6 released. See CHANGELOG

2008-03-14  ·  Version 2.0.5 released. See CHANGELOG

2008-03-06  ·  Server will be down from 2008-03-07 to 2008-03-08.

2008-03-05  ·  Version 2.0.4 released. See CHANGELOG

2008-02-29  ·  Uploaded webpage.