There tools are intended for use with the stand-alone version of the ClustalW application. The application is available for free download here:
ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/
Documentation for ClustalW is available here:
http://www.infobiogen.fr/doc/ClustalW/clustalw_help.html
Tools included are:
CLUSTALWGUI - simple GUI for alignment tasks
@CLUSTALWCMD - class used to store parameters to pass to ClustalW
CALL_CLUSTALW - function that passes the parameters from a @CLUSTALWCMD object to the ClustalW application
CLUSTALALIGNREAD - file for importing the ClustalW formatted alignment file, produced by ClustalW.
Instructions:
Extract the files to a directory on your MATLAB path. You will also need to place the ClustalW application file in a directory on your system's PATH.
An example alignment file (example.aln) is included for use with CLUSTALWGUI. Follow the steps below, to align the example sequences, using the default options.
1) Open the file from CLUSTALWGUI's File menu.
2) Select a location for the output alignment file. For example, 'aligned.aln'.
3) Press the 'ClustalW!' button.
The output from the ClustalW will be displayed to the screen. You can then use CLUSTALALIGNREAD to import the sequences as a structure, including the consensus line:
s = clustalalignread('aligned.aln') |
