Alignment methods
Three different alignment methods are included in the Additional Alignments plugin: ClustalO, ClustalW, and MUSCLE. The included alignment methods and how they are used are very briefly described below. For more detailed information on each of the alignment methods we encourage to read the original research papers and the respective websites of the different methods. The papers [Edgar and Batzoglou, 2006] and [Plyusnin and Holm, 2012] describe the below mentioned algorithms and some of their strengths.
When the Additional Alignments plugin is installed the tools can be found in the toolbox as shown in figure 2.1.
Figure 2.1: The Additional Alignments plugin can be found in the toolbox under "Alignments and Trees".
To create an alignment using an alignment method in the plugin, select sequences to align and go to
Toolbox | Classical Sequence Analysis (
) | Alignments and Trees (
) | Additional Alignments ()
Choose the desired alignment (
). This opens the dialog shown in figure 2.2.
Figure 2.2: Selecting sequences for the alignment.
Subsections