9.2.3 Sequence alignment using ClustalW

ClustalW is a widely used program for performing sequence alignment. ClustalW can be run from within Geneious Prime without having to export or import your sequences.

To perform an alignment using ClustalW, select the sequences or alignment you wish to align, then select Align/Assemble → Multiple Align.... Select ClustalW as the alignment type, and the options available for a ClustalW alignment will be displayed.

The options are:

• Cost Matrix: Use this to select the desired cost matrix for the alignment. The available options here will change according to the type of the sequences you wish to align. You can also click the ‘Custom File’ button to use a cost matrix that you have on your computer (the format of these is the same as for the program BLAST).
• Gap open cost and Gap extend cost: Enter the desired gap costs for the alignment.
• Free end gaps: Select this option to avoid penalizing gaps at either end of the alignment. See details in the Pairwise Alignment section above.
• Preserve original sequence order: Select this option to have the order of the sequences in the table preserved so that the alignment contains the sequences in the same order.
• Additional options: Any additional parameters accepted by the ClustalW command line program can be entered here. Refer to the ClustalW manual for a description of the available parameters.
• Custom ClustalW executable: The ClustalW2 executable is bundled with Geneious so there is no need to download this yourself. However, if you wish to use a different executable from the one within Geneious, you can choose this here.

You can also do a Clustal alignment via translation and back (see section 9.2.6 ).

After entering the desired options click OK and ClustalW will be called to align the selected sequences or alignment. Once complete, a new alignment document will be generated with the result as detailed previously.