Additional alignment plug-in

This extension allows for use of five other alignment methods which are otherwise not distributed with the CLC Workbench.

Alignment methods

Five different alignment methods are included in this extension: ClustalW, Muscle, T-Coffee, Kalign and Mafft. For more detailed information on each of the alignment methods we encourage you to read the original research papers and the respective websites of the different methods. A recent paper describes some of the below mentioned algorithms and their strengths [Edgar and Batzoglou, 2006].

Method	Website	Publication	Platform
ClustalW		Thomsen et al., 1994
Muscle		Edgar, 2004b; Edgar, 2004a
T-Coffee		Notredame et al., 2000
MAFFT		Katoh et al., 2002
Kalign		Lassmann and Sonnhammer, 2005

 

When the plug-in is installed, you will see the new alignment methods in the Toolbox under Alignments and Trees -> External Alignment. When you run the alignments, there are a number of parameters that can be set. You can also specify command line instructions.

Download plug-in:

The plug-in is easily installed from within the Workbench:

1. Click Plug-ins() in the Tool bar .
2. Click the tab Download Plug-ins.
3. Select the plug-in you wish to install.
4. Click the Download and Install button.

Alternatively, you can download the plug-in here.