Bioinformatics toolkit

Third Party Program: ClustalW

Citation:

Thompson J.D., Higgins D.G., Gibson T.J. "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(1994).

Please note that ClustalW is a third party program and not written by the author of these pages.

About Clustalw

ClustalW, a multiple sequence alignment program, is available for download from a number of sites including the EBI FTP Server at http://www.ebi.ac.uk/FTP/. Links specific for your operating system can be found below:

Microsoft Windows users

If the above links do not work, try visiting ftp://ftp.ebi.ac.uk/pub/software/dos/clustalw/ and select the appropriate archive file from here.

To install, simply download the appropriate archive file for your operating system and unpack in a directory of your choice.

Apple Mac OS X users

A pre-compiled version (clustalw1.82.mac-osx.tar.gz) is available from ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/. To install, simply download the appropriate archive file for your operating system and unpack in a directory of your choice.

Alternatively download the archive clustalw1.83.UNIX.tar.gz from ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/ and compile Clustalw yourself by following the same instructions as for Unix/Linux users (see below).

Linux/Unix users

Download the archive clustalw1.83.UNIX.tar.gz or equivalent from ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/ and compile with the following commands:

In a terminal

1) Go to the directory in which the archive was saved. For example, by default Mac OS X saves to the Desktop, in which case you might type:

cd ~/Desktop/

2) If the archive has not yet been unpacked (e.g. with StuffIt on Mac OS X), unpack with the following command:

tar xzvvf clustalw1.83.UNIX.tar.gz

3) The unpacked directory will contain the source files for the Clustalw program. Enter the directory and compile the sources as follows:

cd clustalw1.83/
make

4) If all goes well an executable named 'clustalw' should be created. To test that it works type the following:

./clustalw

And Clustalw should run in your terminal. To exit the program press 'q'.

Clustalw should now be ready to use by the toolkit. The executable can be moved to somewhere more convenient on your system if you want (for example, create a 'bin' directory in your home directory and put it in that).

Apple Mac OS X users

Mac OS X users can get a terminal with the menu options :

Go > Applications > Utilities > Terminal.