Clustal: Multiple Sequence Alignment
Multiple alignment of nucleic acid and protein sequences
Webservers
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 comes in two flavors: the command-line version
ClustalW and the graphical version ClustalX.
Precompiled executables for Linux, Mac OS X and Windows (incl.
XP and Vista) of the
most recent version
(currently 2.0.12)
along with the source code are
available for download here.
You can also browse for
older versions (ClustalW 1.81, ClustalV etc).
The current version of Clustal is also mirrored on the
EBI ftp site
.
Clustal is copyrighted. Please have a look at the license file.
Documentation
Help
Please have a look at ClustalX's builtin help menu or if you
are using ClustalW 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Online versions (which might be out of date) can be found here:
ClustalW
and
ClustalX.
There are a couple of references on how to use
ClustalW/X on the net. A very nice tutorial which also covers
advanced features like using secondary structures for profile
alignment is
"Using ClustalX for multiple sequence"
by Jarno Tuimala
(local mirror).
References
-
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan
PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R,
Thompson JD, Gibson TJ, Higgins DG.
(2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948. -
Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG,
Thompson JD.
(2003). Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res., 31, 3497-3500. -
Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ.
(1998). Multiple sequence alignment with Clustal X. Trends Biochem Sci., 23, 403-405. -
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins
DG.
(1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res., 25, 4876-4882. -
Higgins DG, Thompson JD, Gibson TJ.
(1996). Using CLUSTAL for multiple sequence alignments. Methods Enzymol., 266, 383-402. -
Thompson JD, Higgins DG, Gibson TJ.
(1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680. -
Higgins DG.
(1994). CLUSTAL V: multiple alignment of DNA and protein sequences. Methods Mol Biol., 25, 307-318 -
Higgins DG, Bleasby AJ, Fuchs R.
(1992). CLUSTAL V: improved software for multiple sequence alignment. Comput. Appl. Biosci., 8, 189-191. -
Higgins,DG and Sharp,PM
(1989). Fast and sensitive multiple sequence alignments on a microcomputer. Comput. Appl. Biosci., 5, 151-153. -
Higgins,D.G. and Sharp,P.M.
(1988). CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene, 73, 237-244.
Contact / Bugs
Clustal is currently maintained at the Conway Institute UCD Dublin by Des Higgins, Fabian Sievers 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
- Nexus format
-
Alignments in Nexus format include a faulty line ("symbols=...")
that can lead to misinterpretation by some programs. This will be addressed
in the new release 2.0.13.
In the meantime, please delete this line from the output. Mesquite version 2.73 (available from the start of July 2010) contains a workaround for this problem. - Downloaded files cannot be installed / are corrupted
- If this happens please use the EBI mirror for download (see above)
- Use of secondary structure information in profile alignment mode (ClustalX <= 2.0.12)
-
If you use two files with secondary structure annotation in
profile alignment mode, ClustalX should normally ask you if
you want to use that information to set local gap penalties.
This should happen in a popup window, but instead the
information is written to the command prompt, which you
won't see if you started ClustalX from a menu.
As a workaround start ClustalX manually i.e. from the command prompt in Windows or any type of Terminal on Mac OS X/Linux. When you then load your files in profile mode, check the command prompt. - UPGMA trees cannot be read by some programs (Clustal < 2.0.12)
- Some tree drawing programs cannot read UPGMA trees created by Clustal, e.g. NJplot and TreeView. Other programs like ATV or TreeView X read these tree files without any problems.
- 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.
Acknowledgements
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...
Recent work on Clustal was mainly funded by Science Foundation Ireland
News:
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.