Additional alignment plugin
This extension allows for use of two other alignment methods which are otherwise not distributed with CLC Workbench.
Two different alignment methods are included in this extension: ClustalW and Muscle. 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].
|ClustalW||More information||Thomsen et al., 1994||Cross-platform|
|Muscle||More information||Edgar, 2004b; Edgar, 2004a||Cross-platform|
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.