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:

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.