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.

Image toolbox
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 (Image gene_and_protein_analysis) | Alignments and Trees (Image alignmentsandtrees) | Additional Alignments (Image alignmentsandtrees)

Choose the desired alignment (Image alignment). This opens the dialog shown in figure 2.2.

Image createalignment
Figure 2.2: Selecting sequences for the alignment.