Alignment methods

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].

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.