Three different alignment methods are included in this plugin: ClustalW, ClustalO, 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. This paper describes some of the below mentioned algorithms and their strengths [Edgar and Batzoglou, 2006].
|ClustalW||More information||Thompson et al., 1994||Cross-platform|
|ClustalO||More information||Sievers et al., 2011||Cross-platform|
|Muscle||More information||Edgar, 2004||Cross-platform|
When the plugin is installed, you will see the new alignment methods in the Toolbox under Alignments and Trees -> Additional Alignments.