GPMAW has been prepared for ClustalW since version 6.0. However, due to licencing problems, it has not been possible to include ClustalW in the distribution package, but as the program is freely available for download, its use has been included in GPMAW.
ClustalW in GPMAW has not been strongly advocated because the version of ClustalW that could be downloaded was not compatible with Windows XP. However, this has been corrected, and the installation description follows.
The local executable version of ClustalW is available from a large number of sources on the web, but this is one of the official sites:
The following description is based on Microsoft Internet Explorer, most most other browsers work similarly.
Point your browser to the location above (double click on the link) and a list of files on the FTP server is displayed. Right-click on the file named clustalw1.83.DOS.zip and select ‘Copy to folder...’ from the menu. Select an appropriate directory, copy and decompress the file.
In the directory \gpmaw\bin\ (usually located either in the c:\ root or in c:\program files\) you create a new directory called ClustalW. Into this directory you copy all of the decompressed files from clustalw1.83.DOS.zip. The files having the extension .h and .c are source code files and can be deleted.
If you are working with Windows XP you will need to download the file clustalw1.83.XP.zip and decompress this as well. This file expands to a single file called clustalw.exe. Copy this file into the \gpmaw\bin\clustalw\ directory, replacing the file of the same name.
NOTE: On some Windows 2000 installation, the DOS version of ClustalW does not work. In this case you should install the XP version of ClustalW as described above.
You are now ready to use ClustalW from GPMAW. When working in GPMAW you open the sequences to align on the desktop, select Search | ClustalW from the menu, and you will be greeted by a dialog box where you can select and edit the names of the sequences on the desktop.
When asking GPMAW to align the sequences, the program will call ClustalW.exe (if located correctly in the \gpmaw\bin\clustalw\ directory) and the alignment will take place in the background (GPMAW will show a counter while waiting). After the alignment ClustalW will save to a file on disk, which will be loaded and arranged by GPMAW. Remember to right-click in the window to view options.